Powers Wiki - User contributions [en]

Agarose Gel

2022-07-21T20:25:49Z

Wiki Administrator:

==Preparing 1% Agarose Gel==

#Measure 0.6 g of agarose
# Pour the agarose powder into microwavable flask with 60 mL of 1XTAE buffer
#Microwave for 1- 3 min (until the agarose is completely dissolved)
#Cool down the agarose and add ethidium bromide to a final concentration of approximately 0.2 to 0.5 ug/mL
# Pour the agarose into a gel try with the well comb in place
#Let sit at room temperature for about half an hour

'''N.B''' Ethidium bromide is a known mutagen.

==Running Agarose Gel==

# add running buffer to the gel apparatus
# carefully load samples in to the well
# load marker
#

[[category:Cell_Culturing]]
[[category:Gel]]

Dialysis

2022-07-21T20:25:35Z

Wiki Administrator:

Dialysis

# Grab enough dialysis tubing (or a Float-a-lyzer) to hold your sample. If using tubing, make sure there is extra tubing to fold over and clip.
# Fold one end of the tubing two times and clip it with an alligator clip.
##Optional: Add a styrofoam ring around the tubing to help it float later.
# Insert your sample into the tube.
# Fold the other end of the tubing twice and clip with a second alligator clip.
# Place the sample and tubing into a large beaker. Add enough of the new buffer to completely cover the sample or to make it float without touching the bottom of the beaker.
# Place the beaker into a refrigerator on a stir plate and stir slowly.
# Replace the buffer after 4 hours and 2 more times over the next 16-24 hours.
# The total amount of buffer that the sample is exposed to should be 100x the sample volume.
##Example: 10mL sample dialyzed against 1L of new buffer.

[[category:Protein_Preparation]]

Culture and Passage Cells

2022-07-21T20:25:20Z

Wiki Administrator:

==Culture and passage cells==

* ready to passage when cell confluence to 80% or 90% or when the cell density reaches an average of 2 X 105 cells/cm2

* remove medium by aspiration

* wash cells with PBS to remove the residual medium

* add Trypsin-EDTA (enough to cover the flask surface)

* incubate at 37oC for 5 minutes

* observe by microscope to see cell death

* add 2ml of medium trypsinization

* pipet to detach all cells

* transfer cell suspension to 15 ml tube

* add cell culture medium to new flask

* dilute as appropriate into the flask and mix well

* a seeding density of 4.0 X 104 to 5.0 X 104 viable cells/cm2 is used when subculturing capan-1 cells

* for T-75 use 3 x 106 cells, 100 mm Petri plate (57 cm2 surface area) use 2.3 X106 cells , 60 mm Petri plate (22.1 cm 2 surface area) use 8.8 X 10 5 cells.

* incubate at 37oC

* replace media 2-3 days
[[category:Cell_Culturing]]

1D NMR Titrations

2022-07-21T20:25:01Z

Wiki Administrator:

== Protein Stock Preparation ==
# Make 2.0 mM (2000 uM) HSA stock solution
## Dissolve 130.8 mg of HSA (MW = 65400 g) in 1.0 mL D2O
# Make a set of serial dilutions starting with the 2.0 mM stock (see table 1) (NOTE: at these stock solutions it only takes 10.0 uL of protein sample to give the desired protein concentration in the NMR tube)
# Spin Samples down in mini centrifuge
# Press short button until max speed then release
# Measure the absorbance and generate a standard curve for the new samples.
# Make 10X dilutions (10.0 uL HSA and 990 uL D2O)

'''Table 1:'''
{| class="wikitable"
|-
! Sample No.
! NMR [HSA] (uM)
! [HSA] (uM)
! Volume (n+1) sample (uL)
! Volume of D2O (uL)
|-
| 1
| 0.000
| 0.00
| 0
| 0
|-
| 2
| 0.100
| 5.00
| 500
| 500
|-
| 3
| 0.200
| 10.00
| 500
| 500
|-
| 4
| 0.400
| 20.00
| 667
| 333
|-
| 5
| 0.600
| 30.00
| 750
| 250
|-
| 6
| 0.800
| 40.00
| 800
| 200
|-
| 7
| 1.000
| 50.00
| 500
| 500
|-
| 8
| 2.000
| 100.00
| 667
| 333
|-
| 9
| 3.000
| 150.00
| 750
| 250
|-
| 10
| 4.000
| 200.00
| 667
| 333
|-
| 11
| 6.000
| 300.00
| 750
| 250
|-
| 12
| 8.000
| 400.00
| 800
| 200
|-
| 13
| 10.00
| 500.00
| 833
| 167
|-
| 14
| 12.00
| 600.00
| 857
| 143
|-
| 15
| 14.00
| 700.00
| 875
| 125
|-
| 16
| 16.00
| 800.00
| 889
| 111
|-
| 17
| 18.00
| 900.00
| 900
| 100
|-
| 18
| 20.00
| 1000.00
| 667
| 333
|-
| 19
| 30.00
| 1500.00
| 750
| 250
|-
| 20
| 40.00
| 2000.00
| 130.8 mg
| 1 mL
|}

== Ligand Stock Preparation ==
# Make 50.0 mM Potassium Phosphate buffer at pH 7.0 in D2O
## For 500.0 mL total solution, measure 2.177 g K2HPO4 (MW = 174.18 g/mol) and 1.70 g KH2PO4 (MW = 136.09g/mol) in separate 250.0 mL volumetric flasks and fill to line with 99.9% D2O.
## Spike with 500 uL of TMSP from 10.0 uM stock solution
# Make 500.0 uL fresh ligand stocks at 20.0 mM concentration
## Calculate the mass of ligand needed and dissolve in 500.0 uL of 100% DMSO
# Make 11.0 mL titration stocks
## Single ligands: In Falcon tube add, in order, 10.5 mL Potassium Phosphate buffer, 440 uL 100% DMSO and finally 55 uL of fresh ligand stock.
## Ligand Mixtures: In a Falcon tube add in order: 10.390 mL Potassium Phosphate buffer, 440 uL 100% DMSO and finally 55μL of each fresh ligand stock solution (The 2 non-binders Choline Bromide and Uridine-5’-monophosphate plus the binding ligand)
# Vortex the titration stock solutions to mix

== NMR Sample Preparation ==
# Label 20 1.5 uL centrifuge tubes with the ligand and protein concentration
# To each tube add 490 uL of the ligand titration stock solution
# To each tube add 10 uL of the specific protein stock to the intended sample (i.e. add 10 uL of 400 uM stock to get protein concentration in NMR tube of 8 uM)
# Spin samples down in mini-centrifuge to make sure all sample is in the bottom of tube
# Pipette sample out of centrifuge tubes and into NMR tubes making sure not to get any bubbles
# Run samples on NMR using the ''zgesgp'' pulse program (''1D-FASTNMR'' parameter set) or other comparable method for water pre-saturation

=== Important Notes ===
* This is a general method for preparing samples for NMR titrations and can be amended as needed.
* It has been found that the best protein concentration range is 0.00 uM to 40.0 uM to get a complete binding curve for the majority of ligands. This is only for HSA and is most likely different for different proteins.
* Solution Human Serum Albumin is only good for about fourteen days, make sure to write down the date made and make new sample every 14days as needed
[[category:NMR_Usage|NMR Titrations]]
[[category:Sample_Preparation|NMR Titrations]]

700 MHz NMR checklist

2022-07-21T20:24:22Z

Wiki Administrator:

'''Check in for the NMR 700mHz'''

Make sure the system is accessible, e.g. not being used or under maintenance

Check your belongings on your body and remove anything with ferromagnetic properties such as electronic devices and keep them away from the probe

Go to the Sample Jet and change the operating mode to 5mm shuttle, then load the rack of NMR tubes.

Login to the computer

Start topspin software

Load sample by typing in “sx 101” (or if in rack 2: “sx 201”, etc)

Click on the blank document icon

* Name it: initials-title-date

* Experiment: zgesgp (wipes out the water peak)

* Set solvent

* Check the “getprosol” box

Lock the sample by typing “lock d2o”

* The signal should be at around 75% after you lock it. If it is too low, go to BSMS, click “power” and use the scroll on the mouse to get it to around 75%, then click “standby” on BSMS to save the change.

Shim the sample automatically by typing “topshim”

* If the signal is not at 75%, adjust it in the same way as before. Also you can adjust the shimming manually by going to the BSMS and clicking on “z1”, “z2”, “x”, “y”, “xy”, etc. dimensions and using the scroll on the mouse. Don’t forget to click “standby” after any changes.

Autotune the sample by typing “atma”. To manually autotune, type “atmm”.

Next you need to find the 90° pulse.

* Type P1 and enter “8.0” in the pop-up window

* Type “pulprog” and choose “zg”

* Type “ns 1” (number of scans=1), then type “ds 1” (dummy scans), then type “rg 1” (receiver gain).

* Run the sample by typing “zg”

* To transform FID into spectrum, type “efp”

* Type “apk” to autophase

* Not type “p1”, hit enter and try different numbers (usually between 30-44), type “zg” and “efp” in order and see what number (p1) minimizes the peak the most.

* Once you have found the p1 number that minimizes the peak, divide that number by 4. That number is your 90° pulse.

* Type “edprosol” and set the p1 you found into both pulse widths and hit enter in each one

* Click the “copy to solvent” buton and select all relevant

* Click the “copy to probe” and select all relevant again. A popup window will ask you which cryoprobe you want to use. Choose the one that matches the cryoprobe that is in the top left corner.

* Save then “select all relevant”. Click on “yes” and “ok” whenever it asks you and make sure that you calculate all pulses when it asks. Then close out.

To run IconNMR, type “iconnmr” and choose the automation option and enter the password

Go to the holder that your sample is in. For example if your sample is in the 1st rack and is in the first slot in that rack, then go to A1-101.

Type in the name of your experiment, click on the “No.” space to activate that box, choose your solvent, and choose your experiment.

* Experiment for HSQC: C13HSQCS1SP2 (metab)

* Experiment for HMBC: C-13 HMBC

* Experiment for HSQC-TOCSY: SL-hsqcetf3gpml. Metab

Click on the paramters tab and choose “edit all acquisitions parameters”

* In the TD (data points) for the H dimension enter a number that is between 1024 and 2048 although it’s usually 2048. In the C dimension enter a number that is between 64 and 256 although it’s usually 64.

* In the NS (number of scans), type 32 although it can be 64 and even 128 depending on what you want.

* Type d1 and hit enter and input 1.5 for the relaxation time. *If you are doing the HSQC-TOCSY experiment then make sure you also change the d8 (delay time) to whatever number corresponds to the right hand panel

* Type in “rga” to check the automatic receiver gain

* to automation tab and make sure that the AUNM is set to au-zgonly.

* Then click on the button that says “return to iconNMR”

Copy to the samples as needed. (“edit as needed” )

Highlight all of the samples and click submit

Click “Start” and check the “lock/shim has already been completed box” and make sure that you are starting at your sample (for example: 101).

[[category:NMR_Usage|NMR checklist 700]]

Running SDS-PAGE

2022-07-21T20:22:40Z

Wiki Administrator:

[[category:Gel]]
[[category:Protein_Preparation]]
[[Category:Protein expression]]

[[:File:SDS_PAGE.pdf|SDS PAGE]]

==Running SDS-PAGE==

#Make ready the samples to run
#Make ready the sample running buffer
#Make ready the gel
#Have the SDS-PAGE apparatus
#Place the the gel in the SDS-PAGE stand
#Place the stand with the gel in the SDS-PAGE apparatus bath
#fill the space between the gels with running buffer
#Take off the combs of the gel (take it out gently)
#Load the sample to each well
#Do not use the wells at the left and right end of the gel
#fill the SDS-PAGE apparatus bath with running buffer to the bottom of the gel
#Place the cover of the SDS-PAGE
## '''N.B''' Make sure the correct plug is connected to the correct electrode (red goes to red and black goes to black)
#Plug the cables to the SDS-PAGE apparatus power source
#Turn of the SDS-PAGE power source
#Set to constant voltage
#Use 200 V
#Press the Run button to start the electrophoresis
## The voltage increases to 200 V from 0 V
##For 4% staking gel and 12.5 % separating gel the current reaches 50-60 mA and the power 10 -12 W
##The current the the power decreases in time but not reach zero (if it reaches zero see the troubleshoot)
##For the state type of gel it takes 35 - 40 min

===Troubleshoot===
#The power drops to zero
* really old buffer
* the space in between the gels is not filled with buffer to the top

Running SDS-PAGE

2022-07-21T20:21:54Z

Wiki Administrator:

[[category:Gel]]
[[category:Protein_Preparation]]
[[Category:Protein expression]]

[[:File:SDS_PAGE.pdf|SDS PAGE]]

See also [[SDS-PAGE_Protocol | SDS-PAGE Protocol]]
==Running SDS-PAGE==

#Make ready the samples to run
#Make ready the sample running buffer
#Make ready the gel
#Have the SDS-PAGE apparatus
#Place the the gel in the SDS-PAGE stand
#Place the stand with the gel in the SDS-PAGE apparatus bath
#fill the space between the gels with running buffer
#Take off the combs of the gel (take it out gently)
#Load the sample to each well
#Do not use the wells at the left and right end of the gel
#fill the SDS-PAGE apparatus bath with running buffer to the bottom of the gel
#Place the cover of the SDS-PAGE
## '''N.B''' Make sure the correct plug is connected to the correct electrode (red goes to red and black goes to black)
#Plug the cables to the SDS-PAGE apparatus power source
#Turn of the SDS-PAGE power source
#Set to constant voltage
#Use 200 V
#Press the Run button to start the electrophoresis
## The voltage increases to 200 V from 0 V
##For 4% staking gel and 12.5 % separating gel the current reaches 50-60 mA and the power 10 -12 W
##The current the the power decreases in time but not reach zero (if it reaches zero see the troubleshoot)
##For the state type of gel it takes 35 - 40 min

===Troubleshoot===
#The power drops to zero
* really old buffer
* the space in between the gels is not filled with buffer to the top

OpenEye Software

2022-07-21T20:21:33Z

Wiki Administrator:

This page describes the maintenance and use of the various programs for the OpenEye software suite on your workstation and the cluster.

==Installing OpenEye Packages==
'''You must be root to perform these updates! Doing so under any other user account will break the installation.'''

Every two years, the OpenEye software license expires, forcing the user to acquire a new license and reinstall the packages. First, create an account at eyesopen.com and submit your new license file. Then, proceed to the downloads page and download the following (x86_64, RHEL5) tarballs to somewhere on /DATA which will be referred to as ''$pkgdir'':

* babel
* brood
* eon
* filter
* fred
* lexichem
* ogham
* omega
* quacpac
* rocs
* szybki
* vida

Now, ''ssh'' into bionmr-c1 and ''su'' to root, then '''carefully''' perform the following commands:

cd /home/PROGRAMS/OpenEyeBundle
rm -rf openeye-old
mv -f openeye openeye-old
tar xzf ''${pkgdir}''/babel-*.tar.gz
tar xzf ''${pkgdir}''/brood-*.tar.gz
tar xzf ''${pkgdir}''/eon-*.tar.gz
tar xzf ''${pkgdir}''/filter-*.tar.gz
tar xzf ''${pkgdir}''/fred-*.tar.gz
tar xzf ''${pkgdir}''/lexichem-*.tar.gz
tar xzf ''${pkgdir}''/ogham-*.tar.gz
tar xzf ''${pkgdir}''/omega-*.tar.gz
tar xzf ''${pkgdir}''/quacpac-*.tar.gz
tar xzf ''${pkgdir}''/rocs-*.tar.gz
tar xzf ''${pkgdir}''/szybki-*.tar.gz
tar xzf ''${pkgdir}''/vida-*.tar.gz
cp ''${pkgdir}''/oe_license.txt openeye/
chmod 644 openeye/oe_license.txt
chown -R 502:501 openeye

That should do it.
[[category:Sysadmin]]
[[category:Molecular Docking]]

Category:LC-MS

2022-07-21T20:18:44Z

Wiki Administrator: Blanked the page

Adding Compounds To Bioscreen

2022-07-21T20:15:51Z

Wiki Administrator:

Before compounds are added into the physical FAST-NMR library, they should be added to (or their existence ensured in) the [http://bionmr-c1.unl.edu/cgi-bin/ligands/index Bioscreen Ligands Frontend]. Please don't wait until after you add the compound to make a database entry; it's likely you'll forget. Sorry.

==Checking if the compound exists==
To avoid duplicating compounds in the database, you must check if the new compound already exists in Bioscreen. To do that, use the global search box at the top of the Ligands Frontend pages to search for your compound. Searching all possible names, including the PDB HET identifier and the CAS number, is critical to avoid duplication. You can follow this checklist in order to make sure you aren't duplicating a ligand:

* Use the global (include inactive results) ligand query to search for:
# All possible ligand names
# Substrings of possible ligand names
# PDB HET identifier of the ligand, if one exists
# CAS number of the ligand

Under some rare circumstances, your compound may not have a CAS number. If it does not have a CAS number, use this ligands report to search for all ligands in the database without CAS numbers:
molID, commonName, altNames from ligands where CAS is null

If the compound exists, simply add it into the new plate and well and update its information fields.

==Creating a new compound in the database==
If the compound does not exist in the database, you must create a new compound entry. On the main page of the Ligands Frontend, click on the '''create''' button in the ''Add new ligand'' section. The ligand upload box will appear. Enter the IUPAC Name and the Common Name of the compound, and supply a [[:Wikipedia:Molfile|MOL file]] to the upload box, then click on '''import'''.

If you did everything right and lovingly asked Bioscreen to do your bidding, you should be looking at the view page for your new compound. If you do not supply both the names and the file, or if the file is corrupt or of the incorrect format, Bioscreen will generate an error and your new compound will not be added.

===Finishing the creation===
For the benefit of all Bioscreen users, it is '''imperative''' that all available fields for new compounds be completely filled out. Please take the two minutes required to finish filling out the information for the new compound.

[[Category:Bioscreen]]

Culture Passage Cells

2022-07-21T19:52:20Z

Wiki Administrator: Created page with "==Culture and passage cells== * ready to passage when cell confluence to 80% or 90% or when the cell density reaches an average of 2 X 105 cells/cm2 * remove medium by aspiration * wash cells with PBS to remove the residual medium * add Trypsin-EDTA (enough to cover the flask surface) * incubate at 37oC for 5 minutes * observe by microscope to see cell death * add 2ml of medium trypsinization * pipet to detach all cells * transfer cell suspension to 15 ml tube..."

Powers Wiki:Privacy policy

2022-07-21T19:12:31Z

Wiki Administrator: Created page with "=User Accounts= :Only authorized users are allowed to post on this wiki. =Outside Users= :Outside users are allowed to read and save information. =Use of Data= :Data is kept on a secure server and non-login user information such as ip address is not kept."

=User Accounts=
:Only authorized users are allowed to post on this wiki.

=Outside Users=
:Outside users are allowed to read and save information.

=Use of Data=
:Data is kept on a secure server and non-login user information such as ip address is not kept.

Powers Wiki:General disclaimer

2022-07-21T18:44:16Z

Wiki Administrator: Created page with "Note that all protocols are free to use, but the powers lab is not responsible for problems that may arise from their use."

Note that all protocols are free to use, but the powers lab is not responsible for problems that may arise from their use.

Powers Wiki:About

2022-07-21T18:40:08Z

Wiki Administrator: Created page with "The Powers Lab Wiki is a designated tool for sharing and observing Lab protocols and tips for data processing. The Powers Lab is based in Hamilton Hall at the University of Nebraska Lincoln with many previous and current members working to improve the fields of NMR based protein based structure elucidation and NMR based metabolomics. With many structures being calculated through multiple techniques here in Nebraska. NMR Metabolomics has become the largest interest of t..."

The Powers Lab Wiki is a designated tool for sharing and observing Lab protocols and tips for data processing.

The Powers Lab is based in Hamilton Hall at the University of Nebraska Lincoln with many previous and current members working to improve the fields of NMR based protein based structure elucidation and NMR based metabolomics. With many structures being calculated through multiple techniques here in Nebraska. NMR Metabolomics has become the largest interest of the Powers Lab with multiple coordinated projects and collaborations. Multiple members have designed experimental procedures for extraction and analysis. With a multitude of data analysis software in other programs we have developed analysis software in GNU Octave. With growing support and the simplicity of managing multiple dimensional data MVAPACK was and is still being developed. With expanding capabilities to process and analyze from raw data to results in one place MVAPACK is a unique software.

You can read more about the Powers Lab at our [http://bionmr.unl.edu group website]

MediaWiki:Citizen-footer-desc

2022-07-21T18:17:22Z

Wiki Administrator:

NMR Protein Structures and NMR Metabolomics

MediaWiki:Citizen-footer-desc

2022-07-21T18:11:39Z

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"That is why scientists persist in their investigations, why we struggle so desperately for every bit of knowledge, stay up nights seeking the answer to a problem, climb steepest obstacles to the next fragment of understanding, to finally reach that joyous moment of the kick in the discovery, which is part of the pleasure of finding things out."
- Richard P. Feynman (Nobel Prize in Physics, 1965)

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2022-07-21T18:09:27Z

Wiki Administrator: Created page with "Brought to you by the Powers Lab at the University of Nebraska-Lincoln"

Brought to you by the Powers Lab at the University of Nebraska-Lincoln

MediaWiki:Citizen-footer-desc

2022-07-21T18:07:58Z

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Brought to you by the Powers Lab at the University of Nebraska-Lincoln

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2022-07-21T18:07:22Z

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Edit this text on [[MediaWiki:Citizen-footer-desc]]
edit

Sample Barcoding

2020-02-17T18:52:35Z

Wiki Administrator:

Guide To Make Data Entries In Freezerworks Base 2018 Program For Sample Barcoding And Management
1. Open Freezerworks 2018 program from Desktop
2. Enter username and password at the login screen
a. Username: admin
b. Password: admin
3. Successful login will show the below screen
All entries and searches are done using this window. Each step is outlined below
Section 1: To enter new data into the database
1. Enter the details in the CSV excel file labeled as “Freezerworks Data Import” on the Desktop

2. Enter the values correctly under each column (Case and Spelling sensitive)
a. Freezerworks ID: Enter the number succeeding to the previous entry. All Freezerworks ID should be numbered as 1000XX, where XX is the previous entry number
b. Principal Investigator: Enter the name of the PI. Currently all PI names are listed in the database (See Appendix). To add a new name to the list please refer Section 2
c. Sample Type: Enter the type of sample received. Currently few sample types are listed in the database (See Appendix). To add a new type to the list please refer Section 2
d. LastName: Enter the name of the person who received the sample and is making the entry in the database. The name can be First name or Last name or Name initials. But be consistent in the entry as it is a field that can be used to search.
i. For example: For one project the name is entered as “Amith Maroli” and for a second project, the name is entered as ASM. When a search is conducted to see all the samples received by Amith, if I search using the Received by fieldname Amith, No results will be returned.
e. Project Name: Name of the project the samples belong to.
f. Dropped by: Name of the person who drops the samples or is the contact person in the collaborator PI lab
g. Receive Date: Dates the samples are received
h. Comments: Any comments that needs to be noted for the samples
i. Sample Name: Samples names that needs to be reflected in the database
j. Initial Amount: Volume of sample received
k. Current Amount: Volume of sample left after analysis
l. VolumeUnits: Units (mg, g, mL, uL, L etc.)
3. Save the CSV file.
4. In the FreezerWorks program  Import  CSV Import  Import Settings
5. In the import setting, one can add “New Project and Samples” (Add radio button) or add new samples to existing projects (Add Aliquots to Samples radio button)
6. Click Import (lower left corner) and select the CSV file.
7. Successful import would show a dialog box with the number of records imported or a failed import will show an Error dialog box. Click on “View Error Report” to see what the errors are
Section 2: To enter new information in the fieldnames/enter new entry labels
1. Close all open sub-windows in the FreezerWorks program to get a blank space

2. Click on “Configuration” in the Menu Bar

3. Select “Data Entry and Display” sub-menu

4. To add new fieldnames, select “Fields”
5. List of currently entered fieldnames are displayed

6. To add new field, Click Add new and create the appropriate fieldname either under “Sample” or “Aliquot”. “Sample correspond to the Main projects and Aliqouts corrspond to the samples under the project.

7. To edit an existing field,double click the corresponding fieldname and make the changes.
a. For example: To add a new name to the PI list, double-click the field name “Principal Investigator” and enter the name of the PI on the right side column

8. Similar approach can be done to edit other fields (e.g. Sample Type)

Section 2: To print barcode labels

1. From the main window, select the entry to print the labels

2. Select “BB33_Custom” as the Label Format Name and “Microsoft XPS Writer” as the Printer. Select “Include Aliquots with no assigned Position” and select print to save the .xps file.

3. From the saved location, open the file and select print and then select i3300 printer and adjust the print preferences.

4. In the Preferences menuAdvancedPaper size PropertiesB33-155. Selcet OK for all and then change the Number of copies to 1. Click Print to print the labels

APPENDIX
A. List of Principle Investigators in Selection List
• Alex Vecchio
• Armen Petryosan
• Carol Casey
• Catherine Eichorn
• Charles Wood
• Devine Rose
• Limei Zhang
• Mark Wilson
• NuTek Salt
• Raul Barletta
• Rebecca Wachs
• Robert Powers
• Roberto Deegan
• Srivatsan Kidambi

Sample Barcoding

2020-02-17T18:48:50Z

Wiki Administrator:

Guide To Make Data Entries In Freezerworks Base 2018 Program For Sample Barcoding And Management
1. Open Freezerworks 2018 program from Desktop
2. Enter username and password at the login screen
a. Username: admin
b. Password: admin
3. Successful login will show the below screen
All entries and searches are done using this window. Each step is outlined below
Section 1: To enter new data into the database
1. Enter the details in the CSV excel file labeled as “Freezerworks Data Import” on the Desktop

2. Enter the values correctly under each column (Case and Spelling sensitive)
a. Freezerworks ID: Enter the number succeeding to the previous entry. All Freezerworks ID should be numbered as 1000XX, where XX is the previous entry number
b. Principal Investigator: Enter the name of the PI. Currently all PI names are listed in the database (See Appendix). To add a new name to the list please refer Section 2
c. Sample Type: Enter the type of sample received. Currently few sample types are listed in the database (See Appendix). To add a new type to the list please refer Section 2
d. LastName: Enter the name of the person who received the sample and is making the entry in the database. The name can be First name or Last name or Name initials. But be consistent in the entry as it is a field that can be used to search.
i. For example: For one project the name is entered as “Amith Maroli” and for a second project, the name is entered as ASM. When a search is conducted to see all the samples received by Amith, if I search using the Received by fieldname Amith, No results will be returned.
e. Project Name: Name of the project the samples belong to.
f. Dropped by: Name of the person who drops the samples or is the contact person in the collaborator PI lab
g. Receive Date: Dates the samples are received
h. Comments: Any comments that needs to be noted for the samples
i. Sample Name: Samples names that needs to be reflected in the database
j. Initial Amount: Volume of sample received
k. Current Amount: Volume of sample left after analysis
l. VolumeUnits: Units (mg, g, mL, uL, L etc.)

3. Save the CSV file.

4. In the FreezerWorks program  Import  CSV Import  Import Settings

5. In the import setting, one can add “New Project and Samples” (Add radio button) or add new samples to existing projects (Add Aliquots to Samples radio button)

6. Click Import (lower left corner) and select the CSV file.

7. Successful import would show a dialog box with the number of records imported or a failed import will show an Error dialog box. Click on “View Error Report” to see what the errors are

j)

Section 2: To enter new information in the fieldnames/enter new entry labels

1. Close all open sub-windows in the FreezerWorks program to get a blank space

2. Click on “Configuration” in the Menu Bar

3. Select “Data Entry and Display” sub-menu

4. To add new fieldnames, select “Fields”
5. List of currently entered fieldnames are displayed

6. To add new field, Click Add new and create the appropriate fieldname either under “Sample” or “Aliquot”. “Sample correspond to the Main projects and Aliqouts corrspond to the samples under the project.

7. To edit an existing field,double click the corresponding fieldname and make the changes.
a. For example: To add a new name to the PI list, double-click the field name “Principal Investigator” and enter the name of the PI on the right side column

8. Similar approach can be done to edit other fields (e.g. Sample Type)

Section 2: To print barcode labels

1. From the main window, select the entry to print the labels

2. Select “BB33_Custom” as the Label Format Name and “Microsoft XPS Writer” as the Printer. Select “Include Aliquots with no assigned Position” and select print to save the .xps file.

3. From the saved location, open the file and select print and then select i3300 printer and adjust the print preferences.

4. In the Preferences menuAdvancedPaper size PropertiesB33-155. Selcet OK for all and then change the Number of copies to 1. Click Print to print the labels

APPENDIX
A. List of Principle Investigators in Selection List
• Alex Vecchio
• Armen Petryosan
• Carol Casey
• Catherine Eichorn
• Charles Wood
• Devine Rose
• Limei Zhang
• Mark Wilson
• NuTek Salt
• Raul Barletta
• Rebecca Wachs
• Robert Powers
• Roberto Deegan
• Srivatsan Kidambi

Sample Barcoding

2020-02-17T18:48:21Z

Wiki Administrator:

Guide To Make Data Entries In Freezerworks Base 2018 Program For Sample Barcoding And Management
1. Open Freezerworks 2018 program from Desktop

2. Enter username and password at the login screen
a. Username: admin
b. Password: admin

3. Successful login will show the below screen
All entries and searches are done using this window. Each step is outlined below

Section 1: To enter new data into the database

1. Enter the details in the CSV excel file labeled as “Freezerworks Data Import” on the Desktop

2. Enter the values correctly under each column (Case and Spelling sensitive)
a. Freezerworks ID: Enter the number succeeding to the previous entry. All Freezerworks ID should be numbered as 1000XX, where XX is the previous entry number
b. Principal Investigator: Enter the name of the PI. Currently all PI names are listed in the database (See Appendix). To add a new name to the list please refer Section 2
c. Sample Type: Enter the type of sample received. Currently few sample types are listed in the database (See Appendix). To add a new type to the list please refer Section 2
d. LastName: Enter the name of the person who received the sample and is making the entry in the database. The name can be First name or Last name or Name initials. But be consistent in the entry as it is a field that can be used to search.
i. For example: For one project the name is entered as “Amith Maroli” and for a second project, the name is entered as ASM. When a search is conducted to see all the samples received by Amith, if I search using the Received by fieldname Amith, No results will be returned.
e. Project Name: Name of the project the samples belong to.
f. Dropped by: Name of the person who drops the samples or is the contact person in the collaborator PI lab
g. Receive Date: Dates the samples are received
h. Comments: Any comments that needs to be noted for the samples
i. Sample Name: Samples names that needs to be reflected in the database
j. Initial Amount: Volume of sample received
k. Current Amount: Volume of sample left after analysis
l. VolumeUnits: Units (mg, g, mL, uL, L etc.)

3. Save the CSV file.

4. In the FreezerWorks program  Import  CSV Import  Import Settings

5. In the import setting, one can add “New Project and Samples” (Add radio button) or add new samples to existing projects (Add Aliquots to Samples radio button)

6. Click Import (lower left corner) and select the CSV file.

7. Successful import would show a dialog box with the number of records imported or a failed import will show an Error dialog box. Click on “View Error Report” to see what the errors are

j)

c:::::>

¢:::J

Section 2: To enter new information in the fieldnames/enter new entry labels

1. Close all open sub-windows in the FreezerWorks program to get a blank space

2. Click on “Configuration” in the Menu Bar

3. Select “Data Entry and Display” sub-menu

4. To add new fieldnames, select “Fields”
5. List of currently entered fieldnames are displayed

6. To add new field, Click Add new and create the appropriate fieldname either under “Sample” or “Aliquot”. “Sample correspond to the Main projects and Aliqouts corrspond to the samples under the project.

7. To edit an existing field,double click the corresponding fieldname and make the changes.
a. For example: To add a new name to the PI list, double-click the field name “Principal Investigator” and enter the name of the PI on the right side column

8. Similar approach can be done to edit other fields (e.g. Sample Type)

Section 2: To print barcode labels

1. From the main window, select the entry to print the labels

2. Select “BB33_Custom” as the Label Format Name and “Microsoft XPS Writer” as the Printer. Select “Include Aliquots with no assigned Position” and select print to save the .xps file.

3. From the saved location, open the file and select print and then select i3300 printer and adjust the print preferences.

4. In the Preferences menuAdvancedPaper size PropertiesB33-155. Selcet OK for all and then change the Number of copies to 1. Click Print to print the labels

APPENDIX

A. List of Principle Investigators in Selection List
• Alex Vecchio
• Armen Petryosan
• Carol Casey
• Catherine Eichorn
• Charles Wood
• Devine Rose
• Limei Zhang
• Mark Wilson
• NuTek Salt
• Raul Barletta
• Rebecca Wachs
• Robert Powers
• Roberto Deegan
• Srivatsan Kidambi

Sample Barcoding

2020-02-17T18:46:57Z

Wiki Administrator:

[*http://bionmr.unl.edu/mediawiki/index.php/Category:Protocols link C:\Users\tvu2\Downloads\AA.pdf]

Sample Barcoding

2020-02-17T18:46:01Z

Wiki Administrator: Replaced content with "[*http://http://bionmr.unl.edu/mediawiki/index.php/Category:Protocols link C:\Users\tvu2\Downloads\AA.pdf]"

[*http://http://bionmr.unl.edu/mediawiki/index.php/Category:Protocols link C:\Users\tvu2\Downloads\AA.pdf]

Sample Barcoding

2020-02-17T18:40:01Z

Wiki Administrator:

Guide To Make Data Entries In Freezerworks Base 2018 Program For Sample Barcoding And Management
1. Open Freezerworks 2018 program from Desktop
[[C:\Users\tvu2\Downloads\AA.pdf]]
2. Enter username and password at the login screen
a. Username: admin
b. Password: admin

3. Successful login will show the below screen
All entries and searches are done using this window. Each step is outlined below

Section 1: To enter new data into the database

1. Enter the details in the CSV excel file labeled as “Freezerworks Data Import” on the Desktop

2. Enter the values correctly under each column (Case and Spelling sensitive)
a. Freezerworks ID: Enter the number succeeding to the previous entry. All Freezerworks ID should be numbered as 1000XX, where XX is the previous entry number
b. Principal Investigator: Enter the name of the PI. Currently all PI names are listed in the database (See Appendix). To add a new name to the list please refer Section 2
c. Sample Type: Enter the type of sample received. Currently few sample types are listed in the database (See Appendix). To add a new type to the list please refer Section 2
d. LastName: Enter the name of the person who received the sample and is making the entry in the database. The name can be First name or Last name or Name initials. But be consistent in the entry as it is a field that can be used to search.
i. For example: For one project the name is entered as “Amith Maroli” and for a second project, the name is entered as ASM. When a search is conducted to see all the samples received by Amith, if I search using the Received by fieldname Amith, No results will be returned.
e. Project Name: Name of the project the samples belong to.
f. Dropped by: Name of the person who drops the samples or is the contact person in the collaborator PI lab
g. Receive Date: Dates the samples are received
h. Comments: Any comments that needs to be noted for the samples
i. Sample Name: Samples names that needs to be reflected in the database
j. Initial Amount: Volume of sample received
k. Current Amount: Volume of sample left after analysis
l. VolumeUnits: Units (mg, g, mL, uL, L etc.)

3. Save the CSV file.

4. In the FreezerWorks program  Import  CSV Import  Import Settings

5. In the import setting, one can add “New Project and Samples” (Add radio button) or add new samples to existing projects (Add Aliquots to Samples radio button)

6. Click Import (lower left corner) and select the CSV file.

7. Successful import would show a dialog box with the number of records imported or a failed import will show an Error dialog box. Click on “View Error Report” to see what the errors are

j)

c:::::>

¢:::J

Section 2: To enter new information in the fieldnames/enter new entry labels

1. Close all open sub-windows in the FreezerWorks program to get a blank space

2. Click on “Configuration” in the Menu Bar

3. Select “Data Entry and Display” sub-menu

4. To add new fieldnames, select “Fields”
5. List of currently entered fieldnames are displayed

6. To add new field, Click Add new and create the appropriate fieldname either under “Sample” or “Aliquot”. “Sample correspond to the Main projects and Aliqouts corrspond to the samples under the project.

7. To edit an existing field,double click the corresponding fieldname and make the changes.
a. For example: To add a new name to the PI list, double-click the field name “Principal Investigator” and enter the name of the PI on the right side column

8. Similar approach can be done to edit other fields (e.g. Sample Type)

Section 2: To print barcode labels

1. From the main window, select the entry to print the labels

2. Select “BB33_Custom” as the Label Format Name and “Microsoft XPS Writer” as the Printer. Select “Include Aliquots with no assigned Position” and select print to save the .xps file.

3. From the saved location, open the file and select print and then select i3300 printer and adjust the print preferences.

4. In the Preferences menuAdvancedPaper size PropertiesB33-155. Selcet OK for all and then change the Number of copies to 1. Click Print to print the labels

APPENDIX

A. List of Principle Investigators in Selection List
• Alex Vecchio
• Armen Petryosan
• Carol Casey
• Catherine Eichorn
• Charles Wood
• Devine Rose
• Limei Zhang
• Mark Wilson
• NuTek Salt
• Raul Barletta
• Rebecca Wachs
• Robert Powers
• Roberto Deegan
• Srivatsan Kidambi

Sample Barcoding

2020-02-17T18:33:13Z

Wiki Administrator: Created page with "Guide To Make Data Entries In Freezerworks Base 2018 Program For Sample Barcoding And Management 1. Open Freezerworks 2018 program from Desktop 2. Enter username and password..."

Guide To Make Data Entries In Freezerworks Base 2018 Program For Sample Barcoding And Management
1. Open Freezerworks 2018 program from Desktop

2. Enter username and password at the login screen
a. Username: admin
b. Password: admin

3. Successful login will show the below screen
All entries and searches are done using this window. Each step is outlined below

Section 1: To enter new data into the database

1. Enter the details in the CSV excel file labeled as “Freezerworks Data Import” on the Desktop

2. Enter the values correctly under each column (Case and Spelling sensitive)
a. Freezerworks ID: Enter the number succeeding to the previous entry. All Freezerworks ID should be numbered as 1000XX, where XX is the previous entry number
b. Principal Investigator: Enter the name of the PI. Currently all PI names are listed in the database (See Appendix). To add a new name to the list please refer Section 2
c. Sample Type: Enter the type of sample received. Currently few sample types are listed in the database (See Appendix). To add a new type to the list please refer Section 2
d. LastName: Enter the name of the person who received the sample and is making the entry in the database. The name can be First name or Last name or Name initials. But be consistent in the entry as it is a field that can be used to search.
i. For example: For one project the name is entered as “Amith Maroli” and for a second project, the name is entered as ASM. When a search is conducted to see all the samples received by Amith, if I search using the Received by fieldname Amith, No results will be returned.
e. Project Name: Name of the project the samples belong to.
f. Dropped by: Name of the person who drops the samples or is the contact person in the collaborator PI lab
g. Receive Date: Dates the samples are received
h. Comments: Any comments that needs to be noted for the samples
i. Sample Name: Samples names that needs to be reflected in the database
j. Initial Amount: Volume of sample received
k. Current Amount: Volume of sample left after analysis
l. VolumeUnits: Units (mg, g, mL, uL, L etc.)

3. Save the CSV file.

4. In the FreezerWorks program  Import  CSV Import  Import Settings

5. In the import setting, one can add “New Project and Samples” (Add radio button) or add new samples to existing projects (Add Aliquots to Samples radio button)

6. Click Import (lower left corner) and select the CSV file.

7. Successful import would show a dialog box with the number of records imported or a failed import will show an Error dialog box. Click on “View Error Report” to see what the errors are

j)

c:::::>

¢:::J

Section 2: To enter new information in the fieldnames/enter new entry labels

1. Close all open sub-windows in the FreezerWorks program to get a blank space

2. Click on “Configuration” in the Menu Bar

3. Select “Data Entry and Display” sub-menu

4. To add new fieldnames, select “Fields”
5. List of currently entered fieldnames are displayed

6. To add new field, Click Add new and create the appropriate fieldname either under “Sample” or “Aliquot”. “Sample correspond to the Main projects and Aliqouts corrspond to the samples under the project.

7. To edit an existing field,double click the corresponding fieldname and make the changes.
a. For example: To add a new name to the PI list, double-click the field name “Principal Investigator” and enter the name of the PI on the right side column

8. Similar approach can be done to edit other fields (e.g. Sample Type)

Section 2: To print barcode labels

1. From the main window, select the entry to print the labels

2. Select “BB33_Custom” as the Label Format Name and “Microsoft XPS Writer” as the Printer. Select “Include Aliquots with no assigned Position” and select print to save the .xps file.

3. From the saved location, open the file and select print and then select i3300 printer and adjust the print preferences.

4. In the Preferences menuAdvancedPaper size PropertiesB33-155. Selcet OK for all and then change the Number of copies to 1. Click Print to print the labels

APPENDIX

A. List of Principle Investigators in Selection List
• Alex Vecchio
• Armen Petryosan
• Carol Casey
• Catherine Eichorn
• Charles Wood
• Devine Rose
• Limei Zhang
• Mark Wilson
• NuTek Salt
• Raul Barletta
• Rebecca Wachs
• Robert Powers
• Roberto Deegan
• Srivatsan Kidambi

Category:Protocols

2020-02-17T15:59:20Z

Wiki Administrator:

''General Maintenance''
*[[Changing the high pressure dewar]]
*[[Filling a Magnet with Nitrogen]]
*[[Autoclaving Laboratory Glassware and Media]]
*[[Chemical Disinfection of Glassware]]
*[[Requesting Balance Calibration]]
*[[Requesting Pipette Calibration]]
*[[Using the UV-Vis]]
*[[Using and Maintaining pH Meter]]
*[[-80 Freezer Storage and Maintenance]]
*[[Freeze Dryer Maintenance]]
*[[Lab Notebook Guidelines]]
*[[Sample Barcoding]]

''Protein Preparation''
*[[Buffer Exchange and Solution Concentration]]
*[[Finding a Protein Target on the NESG website]]
*[[Choosing a Plasmid]]
*[[Plasmid Purification and Transformation Protocol]]
*[[Creating Stock Cultures of Bacteria]]
*[[Luria-Bertani Media]]
*[[M9 Minimal Media]]
*[[Protein Overexpression and Extraction]]
*[[SDS-PAGE Protocol]]
*[[Running a Cobalt Affinity Column]]
*[[Dialysis]]
*[[Centrifugal Protein Concentration and Buffer Exchange]]
*[[Using the Stirred Cell Concentrator]]

''Data Collection''
*[[Gap Sampling]]
*[[Water Suppression with presaturation pulses (zgpr/zgcppr]]
*[[Non-uniform Sampling]]
*[[Collecting a 15N Edited HSQC]]
*[[Collecting CEST Data]]

''Data Processing and Analysis''
*[[Analysis of 1D Line-Broadening Screen]]
*[[FastModelFree]]
*[[2D NMR Analysis (CCPNMR)]]
*[[1H NMR Analysis (SIMCA)]]
*[[1H NMR Analysis (ACDLab)]]
*[[Processing CEST Data]]
*[[Titration Data Analysis in nmrPipe]]
*[[Non-Uniform Sampling]]
*[[NMRFAM-SPARKY Guide]]
*[[NMRFAM-SPARKY: Automated Peak Assignment]]
*[[NMR Processing in Linux and Windows]]
*[[Sample Collection and Processing for Protein Backbone Assignments]]
*[[Example Scripts for NMRPipe Processing]]

''Miscellaneous''
*[[Agarose Gel]]
*[[700 MHz NMR checklist]]
*[[500 MHz NMR checklist]]
*[[1D Macro]]
*[[Setting Up a Virtual Screen with AutoDock]]
*[[Simple Protein Crosslinking]]
*[[1D NMR Titrations]]

Cell Culturing
*[[Cell Culturing Dr. Franco Lab]]

''Metabolomics''
*[[MetPa for metabolomics]]
*[[Making Heatmaps]]
*[[Metabolite Extraction]]
*[[One way ANOVA in R]]
*[[P-Value adjustment for multiple comparisons]]
*[[PCA-Utils]]
*[[NMR Tube Deep Cleaning]]
*[[Noise Removal for PCA]]
*[[Weighted Linear Least Squares]]
*[[Serum Preparation for 1D NMR]]
*[[Urine Preparation for 1D NMR]]

''Safety and Inspections''
*[[Lab Responsibilities]]
*[[Inspection Checklist]]
*[[Safety Contacts, Resources]]

''Demos''
*[[Peroxide Clock]]
*[[Traffic Light Reaction]]
*[[Orange Juice Clock]]
*[[Gummy Bear Freeze]]
*[[Batteries]]
*[[Rocket Launcher]]
*[[Women in Science: Checklist]]
*[[Maxey Day: Checklist]]

Generating Protein Structure Statistics Table

2013-12-15T18:17:16Z

Wiki Administrator:

[[Media:Example.ogg]][[category:Protocols]]
= Definitions =
# <SA> is an ensemble of the "best" 30 simulated annealing structures
# SA is average structure
# (SA)r is the restrained minimized average structures
= Experimental: Python table calculator =
Run the following commands if you want to try the automagic structure statistics table calculator:

cd /path/to/my/structure/calculation/files
/home/bworley/research/struct-stats/pull
vi options.py
./Table.py
cat table.txt

The step in which '''options.py''' is edited is the most critical. All the files required by the calculator must be available in the current working directory and accessible by the filenames stored in the options file.

Use at your own risk. If it doesn't work, it doesn't work. If it does work, it will complete all tasks described below except the PROCHECK analysis.

= Manual Method: Use a set of old scripts =
All script files required by this method are stored in '''/home/PROGRAMS/XPLOR_FILES/analysis'''.
==RMS Deviations from Experimental Distance Restraints==
# NOE.cor file needs to be subdivided into separate files containing different constraints classes
## interresidue sequential NOEs (|i-j|=1)
### use awk script: seq_sel.awk '''awk -f seq_sel.awk NOE.cor > seq.cor''' 
### the total number of constraints in the seq.cor file will be listed at the end
## interresidue short range (1 <|i-j| < 5)
### use awk script: short_sel.awk '''awk -f short_sel.awk NOE.cor > short.cor''' 
### the total number of constraints in the short.cor file will be listed at the end
## interresidue long range (1 <|i-j| > 5)
### use awk scrihortpt: long_sel.awk '''awk -f long_sel.awk NOE.cor > long.cor''' 
### the total number of constraints in the long.cor file will be listed at the end
## intraresidue
### use awk script: intra_sel.awk '''awk -f intra_sel.awk NOE.cor > intra.cor''' 
### the total number of constraints in the intra.cor file will be listed at the end
## H-bonds
### These constraints need to be hand collated and counted into the file h-bonds.cor 
### They should all be located in one region (end) of the original NOE.cor file 
# Edit energy.inp and energy_ave.inp to include the filenames for your PSF file, 30 best structures (energy) and restrained minimized structure (energy_ave). 
# Run XPLOR and parse output file:
## '''xplor < energy_ave.inp >& energy.out &'''
## '''csh stat.csh > stat_ave.out'''
## '''cp energy.out energy_ave.out'''
## ''' xplor < energy.inp >& energy.out &'''
## ''' csh stat.csh > stat.out'''
# The files stat.out and stat_ave.out contain the rms deviations from experimental distance restraints for the table.
## A typical stat.out file will looke like: ''RMS_NOE- Column 6 mean: 0.0410533 Std Dev 0.00483168 (N= 30 )'' ''RMS_CDIH- Column 6 mean: 1.43315 Std Dev 0.794072 (N= 30 )'' ''RMS_BONDS (1993)- Column 6 mean: 0.00519457 Std Dev 0.000252635 (N= 30 )'' ''RMS_ANGLES (3655)- Column 6 mean: 0.621244 Std Dev 0.030363 (N= 30 )'' ''RMS_IMPROPERS (972)- Column 6 mean: 0.518672 Std Dev 0.0634619 (N= 30 ) ''RMS_NOE_H-BONDS- Column 7 mean: 0.0958333 Std Dev 0.0133618 (N= 30 )'' ''RMS_NOE_INTRA- Column 7 mean: 0.0075 Std Dev 0.00455887 (N= 30 )'' ''RMS_NOE_LONG- Column 7 mean: 0.0451 Std Dev 0.00898647 (N= 30 )'' ''RMS_NOE_SEQ- Column 7 mean: 0.0378333 Std Dev 0.00800451 (N= 30 )'' ''RMS_NOE_SHORT- Column 7 mean: 0.0427 Std Dev 0.00536128 (N= 30 )'' ''ENERGY_BOND- Column 7 mean: 53.9053 Std Dev 5.35852 (N= 60 )'' ''ENERGY_ANGLE- Column 9 mean: 215.364 Std Dev 21.6272 (N= 60 )'' ''ENERGY_IMPR- Column 5 mean: 40.4231 Std Dev 10.4815 (N= 30 )'' ''ENERGY_REP- Column 8 mean: 107.973 Std Dev 23.6387 (N= 30 )'' ''ENERGY_LJ- Column 8 mean: -374.082 Std Dev 21.1904 (N= 30 )'' ''ENERGY_CDIH- Column 5 mean: 35.9804 Std Dev 45.4492 (N= 30 )'' ''ENERGY_NOE- Column 8 mean: 234.949 Std Dev 57.3573 (N= 30 )''}} 
##rms deviations from experimental distance restraints from the stat.out file
###all ''RMS_NOE- Column 6 mean: 0.0410533 Std Dev 0.00483168 (N= 30 )'' 
###interresidue sequential (|i-j| = 1) ''RMS_NOE_SEQ- Column 7 mean: 0.0378333 Std Dev 0.00800451 (N= 30 )'' 
###interresidue long-range (|i-j| > 5) ''RMS_NOE_LONG- Column 7 mean: 0.0451 Std Dev 0.00898647 (N= 30 )'' 
###Intraresidue ''RMS_NOE_INTRA- Column 7 mean: 0.0075 Std Dev 0.00455887 (N= 30 )'' 
###H-bonds ''RMS_NOE_H-BONDS- Column 7 mean: 0.0958333 Std Dev 0.0133618 (N= 30 )'' 
==RMS Deviation from Experimental Dihedral Restraints (deg)==
# Include the appropriate dihedral contraint (dihed.tbl) file in the energy.inp file used above.
#The value is reported in the stat.out file: ''RMS_CDIH- Column 6 mean: 1.43315 Std Dev 0.794072 (N= 30 )'' 
# To count the number of dihedral restraints used to refine the structure, use the awk script cnt_ang.nawk '''awk –f cnt_ang.nawk dihed.tbl''' 
==RMS Deviation from Experimental Cα Restraints (ppm)==
#Use the CARB_AVE.nawk awk script to parse the ''best'' 30 simulated annealing structures '''awk -f CARB_AVE.nawk *dg*.sam''' 
## *dg*.sam is the wild-card representation of the list of 30 simulated annealing structures
## Please use the proper representation to list your 30 best structures
# Typical output of CARB_AVE.nawk ''Average CA RMS: 0.885654 +/- 0.0299637 For 30 values.'' ''Average CB RMS: 0.905546 +/- 0.0229673 For 30 values.'' ''Average J RMS: 0.606855 +/- 0.04947 For 30 values.'' 
# To count the number of Cα carbon restrains used to refine the structure, us the awk script cnt_ang.nawk '''awk -f cnt_carbon.nawk carbon.tbl 
# This approach can be repeated to determine rms deviation from experimental Cβ restraints (ppm)
==RMS Deviation from 3JNHα Restrains (Hz)==
# Same approach as '''RMS Deviation from Experimental Cα Restraints (ppm)'''
#To count the number of coupling restraints used to refine the structure, use the awk script cnt_coupling.nawk '''awk -f cnt_coupling.nawk coupling.tbl 
==Structure Energies==
# FNOE (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_NOE- Column 8 mean: 234.949 Std Dev 57.3573 (N= 30 )'' 
#Ftor (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_CDIH- Column 5 mean: 35.9804 Std Dev 45.4492 (N= 30 )'' 
#Frepel (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_REP- Column 8 mean: 107.973 Std Dev 23.6387 (N= 30 )'' 
#FL-J (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_LJ- Column 8 mean: -374.082 Std Dev 21.1904 (N= 30 )'' 
==Deviations from Idealized Covalent Geometry==
# bonds (Å)
## The value is reported in the stat.out (see above): ''RMS_BONDS (1993)- Column 6 mean: 0.00519457 Std Dev 0.000252635 (N= 30 )'' 
## The number of bonds is the value in the parenthesis
### 1993 in the example above 
# angles (deg)
## The value is reported in the stat.out file (see above): ''RMS_ANGLES (3655)- Column 6 mean: 0.621244 Std Dev 0.030363 (N= 30 )'' 
## The number of angles is the value in the parenthesis
### 3655 in the example above 
# impropers (deg)
## The value is reported in the stat.out file (see above): ''RMS_IMPROPERS (972)- Column 6 mean: 0.518672 Std Dev 0.0634619 (N= 30 )'' 
## The number of improper dihedral angles is the value in the paranthesis
### 972 in the example 
==PROCHECK==
# Run PROCHECK on each individual structure file from the list of 30 Best Structures '''procheck structure filename 1.0''' 
# Calculate averages and standard deviations using awk script PRO_AVE.nawk '''awk -f PRO_AVE.nawk *dg*.sum''' 
## *dg*sum is the list of procheck output *.sum files for each of the 30 Best Structures
## Make sure the wild-card form only selects for the correct 30 structures
## Typical output: ''Average rama RMS: 83.5167 +/- 2.5297 For 30 values.'' ''Average G-factors RMS: -0.107333 +/- 0.0287441 For 30 values.'' ''Average bad contacts RMS: 17.5 +/- 2.53969 For 30 values.'' 
## Overall G-Factor: ''Average G-factors RMS: -0.107333 +/- 0.0287441 For 30 values.'' 
## %Residues in most favorable region of Ramachandran plot ''Average rama RMS: 83.5167 +/- 2.5297 For 30 values.'' 
## Number of bad contacts/100 residues ''Average bad contacts RMS: 17.5 +/- 2.53969 For 30 values.'' 
### Number needs to be scaled to 100 residues. Multiply by 100/number of residues. 
# Calculate averages and standard deviations using awk script PRO_AVE_2.nawk ''' awk -f PRO_AVE_2.nawk *dg*.out''' 
## *dg*.out is the list of procheck output *.out files for each of the 30 Best Structures
## Make sure the wild-card form only selects for the correct 30 structures
## Typical output: ''Average hbond RMS: 1.04333 +/- 0.0558768 For 30 values.'' 
## The above result is the H-bond energy 
==Atomic RMS Differences==
# Use the rmsdiff.inp and rmsdiff_sec.inp XPLOR scripts
# Repeat the calculates twice, once with the average structure (SA) as the reference structure and the other time with the restrained minimized average structures (SA)r as the reference structure
## Evaluate ($1 = "reference structure name")
# Include the 30 best structures, the average structure and the restrained minimized average structure names in the for loop
# Exclude regions of poorly defined structure in the select statments for both the fit and rms calculations
# Only include regions of α-helix and/or β-sheets in the rmsdiff_sec.inp for both the fit and rms calculations
# Use the awk script average.nawk to calculate the average and standard deviation of the 30 Best Structures '''awk –f average.nawk back_all.rms''' 
## rmsd for backbone atoms
## back_sec.rms output file for rmsdiff_sec.inp file
## Make sure only the 30 Best Structures are list in file
### Need to delete results for average and restrained minimized average structure from back_all.rms
### Make backup first
### Record (SA)r vs SA rmsd values before deleting
### Typical output: ''Average RMS: 0.408533 +/- 0.056732 For 30 values.'' 
# Use average.nawk awk script '''awk –f average.nawk all_all.rms''' 
## rmsd for all atoms
## all_sec.rms output file for rmsdiff_sec.inp file
## Make sure only the 30 Best Structures are listed in file
### Need to delete results for average and restrained minimized average structure
### Make backup first
### Record (SA)r vs SA rmsd values before deleting
### Typical output ''Average RMS: 1.00183 +/- 0.0711051 For 30 values.'' 

==Example Structural Statistics Table==

[[File:Structure_energy_table.doc]]

Generating Protein Structure Statistics Table

2013-12-15T18:17:04Z

Wiki Administrator:

[[Media:Example.ogg]][[category:Protocols]]
==Definitions==
# <SA> is an ensemble of the "best" 30 simulated annealing structures
# SA is average structure
# (SA)r is the restrained minimized average structures
= Experimental: Python table calculator =
Run the following commands if you want to try the automagic structure statistics table calculator:

cd /path/to/my/structure/calculation/files
/home/bworley/research/struct-stats/pull
vi options.py
./Table.py
cat table.txt

The step in which '''options.py''' is edited is the most critical. All the files required by the calculator must be available in the current working directory and accessible by the filenames stored in the options file.

Use at your own risk. If it doesn't work, it doesn't work. If it does work, it will complete all tasks described below except the PROCHECK analysis.

= Manual Method: Use a set of old scripts =
All script files required by this method are stored in '''/home/PROGRAMS/XPLOR_FILES/analysis'''.
==RMS Deviations from Experimental Distance Restraints==
# NOE.cor file needs to be subdivided into separate files containing different constraints classes
## interresidue sequential NOEs (|i-j|=1)
### use awk script: seq_sel.awk '''awk -f seq_sel.awk NOE.cor > seq.cor''' 
### the total number of constraints in the seq.cor file will be listed at the end
## interresidue short range (1 <|i-j| < 5)
### use awk script: short_sel.awk '''awk -f short_sel.awk NOE.cor > short.cor''' 
### the total number of constraints in the short.cor file will be listed at the end
## interresidue long range (1 <|i-j| > 5)
### use awk scrihortpt: long_sel.awk '''awk -f long_sel.awk NOE.cor > long.cor''' 
### the total number of constraints in the long.cor file will be listed at the end
## intraresidue
### use awk script: intra_sel.awk '''awk -f intra_sel.awk NOE.cor > intra.cor''' 
### the total number of constraints in the intra.cor file will be listed at the end
## H-bonds
### These constraints need to be hand collated and counted into the file h-bonds.cor 
### They should all be located in one region (end) of the original NOE.cor file 
# Edit energy.inp and energy_ave.inp to include the filenames for your PSF file, 30 best structures (energy) and restrained minimized structure (energy_ave). 
# Run XPLOR and parse output file:
## '''xplor < energy_ave.inp >& energy.out &'''
## '''csh stat.csh > stat_ave.out'''
## '''cp energy.out energy_ave.out'''
## ''' xplor < energy.inp >& energy.out &'''
## ''' csh stat.csh > stat.out'''
# The files stat.out and stat_ave.out contain the rms deviations from experimental distance restraints for the table.
## A typical stat.out file will looke like: ''RMS_NOE- Column 6 mean: 0.0410533 Std Dev 0.00483168 (N= 30 )'' ''RMS_CDIH- Column 6 mean: 1.43315 Std Dev 0.794072 (N= 30 )'' ''RMS_BONDS (1993)- Column 6 mean: 0.00519457 Std Dev 0.000252635 (N= 30 )'' ''RMS_ANGLES (3655)- Column 6 mean: 0.621244 Std Dev 0.030363 (N= 30 )'' ''RMS_IMPROPERS (972)- Column 6 mean: 0.518672 Std Dev 0.0634619 (N= 30 ) ''RMS_NOE_H-BONDS- Column 7 mean: 0.0958333 Std Dev 0.0133618 (N= 30 )'' ''RMS_NOE_INTRA- Column 7 mean: 0.0075 Std Dev 0.00455887 (N= 30 )'' ''RMS_NOE_LONG- Column 7 mean: 0.0451 Std Dev 0.00898647 (N= 30 )'' ''RMS_NOE_SEQ- Column 7 mean: 0.0378333 Std Dev 0.00800451 (N= 30 )'' ''RMS_NOE_SHORT- Column 7 mean: 0.0427 Std Dev 0.00536128 (N= 30 )'' ''ENERGY_BOND- Column 7 mean: 53.9053 Std Dev 5.35852 (N= 60 )'' ''ENERGY_ANGLE- Column 9 mean: 215.364 Std Dev 21.6272 (N= 60 )'' ''ENERGY_IMPR- Column 5 mean: 40.4231 Std Dev 10.4815 (N= 30 )'' ''ENERGY_REP- Column 8 mean: 107.973 Std Dev 23.6387 (N= 30 )'' ''ENERGY_LJ- Column 8 mean: -374.082 Std Dev 21.1904 (N= 30 )'' ''ENERGY_CDIH- Column 5 mean: 35.9804 Std Dev 45.4492 (N= 30 )'' ''ENERGY_NOE- Column 8 mean: 234.949 Std Dev 57.3573 (N= 30 )''}} 
##rms deviations from experimental distance restraints from the stat.out file
###all ''RMS_NOE- Column 6 mean: 0.0410533 Std Dev 0.00483168 (N= 30 )'' 
###interresidue sequential (|i-j| = 1) ''RMS_NOE_SEQ- Column 7 mean: 0.0378333 Std Dev 0.00800451 (N= 30 )'' 
###interresidue long-range (|i-j| > 5) ''RMS_NOE_LONG- Column 7 mean: 0.0451 Std Dev 0.00898647 (N= 30 )'' 
###Intraresidue ''RMS_NOE_INTRA- Column 7 mean: 0.0075 Std Dev 0.00455887 (N= 30 )'' 
###H-bonds ''RMS_NOE_H-BONDS- Column 7 mean: 0.0958333 Std Dev 0.0133618 (N= 30 )'' 
==RMS Deviation from Experimental Dihedral Restraints (deg)==
# Include the appropriate dihedral contraint (dihed.tbl) file in the energy.inp file used above.
#The value is reported in the stat.out file: ''RMS_CDIH- Column 6 mean: 1.43315 Std Dev 0.794072 (N= 30 )'' 
# To count the number of dihedral restraints used to refine the structure, use the awk script cnt_ang.nawk '''awk –f cnt_ang.nawk dihed.tbl''' 
==RMS Deviation from Experimental Cα Restraints (ppm)==
#Use the CARB_AVE.nawk awk script to parse the ''best'' 30 simulated annealing structures '''awk -f CARB_AVE.nawk *dg*.sam''' 
## *dg*.sam is the wild-card representation of the list of 30 simulated annealing structures
## Please use the proper representation to list your 30 best structures
# Typical output of CARB_AVE.nawk ''Average CA RMS: 0.885654 +/- 0.0299637 For 30 values.'' ''Average CB RMS: 0.905546 +/- 0.0229673 For 30 values.'' ''Average J RMS: 0.606855 +/- 0.04947 For 30 values.'' 
# To count the number of Cα carbon restrains used to refine the structure, us the awk script cnt_ang.nawk '''awk -f cnt_carbon.nawk carbon.tbl 
# This approach can be repeated to determine rms deviation from experimental Cβ restraints (ppm)
==RMS Deviation from 3JNHα Restrains (Hz)==
# Same approach as '''RMS Deviation from Experimental Cα Restraints (ppm)'''
#To count the number of coupling restraints used to refine the structure, use the awk script cnt_coupling.nawk '''awk -f cnt_coupling.nawk coupling.tbl 
==Structure Energies==
# FNOE (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_NOE- Column 8 mean: 234.949 Std Dev 57.3573 (N= 30 )'' 
#Ftor (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_CDIH- Column 5 mean: 35.9804 Std Dev 45.4492 (N= 30 )'' 
#Frepel (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_REP- Column 8 mean: 107.973 Std Dev 23.6387 (N= 30 )'' 
#FL-J (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_LJ- Column 8 mean: -374.082 Std Dev 21.1904 (N= 30 )'' 
==Deviations from Idealized Covalent Geometry==
# bonds (Å)
## The value is reported in the stat.out (see above): ''RMS_BONDS (1993)- Column 6 mean: 0.00519457 Std Dev 0.000252635 (N= 30 )'' 
## The number of bonds is the value in the parenthesis
### 1993 in the example above 
# angles (deg)
## The value is reported in the stat.out file (see above): ''RMS_ANGLES (3655)- Column 6 mean: 0.621244 Std Dev 0.030363 (N= 30 )'' 
## The number of angles is the value in the parenthesis
### 3655 in the example above 
# impropers (deg)
## The value is reported in the stat.out file (see above): ''RMS_IMPROPERS (972)- Column 6 mean: 0.518672 Std Dev 0.0634619 (N= 30 )'' 
## The number of improper dihedral angles is the value in the paranthesis
### 972 in the example 
==PROCHECK==
# Run PROCHECK on each individual structure file from the list of 30 Best Structures '''procheck structure filename 1.0''' 
# Calculate averages and standard deviations using awk script PRO_AVE.nawk '''awk -f PRO_AVE.nawk *dg*.sum''' 
## *dg*sum is the list of procheck output *.sum files for each of the 30 Best Structures
## Make sure the wild-card form only selects for the correct 30 structures
## Typical output: ''Average rama RMS: 83.5167 +/- 2.5297 For 30 values.'' ''Average G-factors RMS: -0.107333 +/- 0.0287441 For 30 values.'' ''Average bad contacts RMS: 17.5 +/- 2.53969 For 30 values.'' 
## Overall G-Factor: ''Average G-factors RMS: -0.107333 +/- 0.0287441 For 30 values.'' 
## %Residues in most favorable region of Ramachandran plot ''Average rama RMS: 83.5167 +/- 2.5297 For 30 values.'' 
## Number of bad contacts/100 residues ''Average bad contacts RMS: 17.5 +/- 2.53969 For 30 values.'' 
### Number needs to be scaled to 100 residues. Multiply by 100/number of residues. 
# Calculate averages and standard deviations using awk script PRO_AVE_2.nawk ''' awk -f PRO_AVE_2.nawk *dg*.out''' 
## *dg*.out is the list of procheck output *.out files for each of the 30 Best Structures
## Make sure the wild-card form only selects for the correct 30 structures
## Typical output: ''Average hbond RMS: 1.04333 +/- 0.0558768 For 30 values.'' 
## The above result is the H-bond energy 
==Atomic RMS Differences==
# Use the rmsdiff.inp and rmsdiff_sec.inp XPLOR scripts
# Repeat the calculates twice, once with the average structure (SA) as the reference structure and the other time with the restrained minimized average structures (SA)r as the reference structure
## Evaluate ($1 = "reference structure name")
# Include the 30 best structures, the average structure and the restrained minimized average structure names in the for loop
# Exclude regions of poorly defined structure in the select statments for both the fit and rms calculations
# Only include regions of α-helix and/or β-sheets in the rmsdiff_sec.inp for both the fit and rms calculations
# Use the awk script average.nawk to calculate the average and standard deviation of the 30 Best Structures '''awk –f average.nawk back_all.rms''' 
## rmsd for backbone atoms
## back_sec.rms output file for rmsdiff_sec.inp file
## Make sure only the 30 Best Structures are list in file
### Need to delete results for average and restrained minimized average structure from back_all.rms
### Make backup first
### Record (SA)r vs SA rmsd values before deleting
### Typical output: ''Average RMS: 0.408533 +/- 0.056732 For 30 values.'' 
# Use average.nawk awk script '''awk –f average.nawk all_all.rms''' 
## rmsd for all atoms
## all_sec.rms output file for rmsdiff_sec.inp file
## Make sure only the 30 Best Structures are listed in file
### Need to delete results for average and restrained minimized average structure
### Make backup first
### Record (SA)r vs SA rmsd values before deleting
### Typical output ''Average RMS: 1.00183 +/- 0.0711051 For 30 values.'' 

==Example Structural Statistics Table==

[[File:Structure_energy_table.doc]]

Generating Protein Structure Statistics Table

2013-12-15T18:12:48Z

Wiki Administrator: /* Experimental: Python table calculator */

[[Media:Example.ogg]][[category:Protocols]]
==Definitions==
# <SA> is an ensemble of the "best" 30 simulated annealing structures
# SA is average structure
# (SA)r is the restrained minimized average structures
= Experimental: Python table calculator =
Run the following commands if you want to try the automagic structure statistics table calculator:

cd /path/to/my/structure/calculation/files
/home/bworley/research/struct-stats/pull
vi options.py
./Table.py
cat table.txt

The step in which '''options.py''' is edited is the most critical. All the files required by the calculator must be available in the current working directory and accessible by the filenames stored in the options file.

Use at your own risk. If it doesn't work, it doesn't work. If it does work, it will complete all tasks described below except the PROCHECK analysis.

==Location of XPLOR, awk and csh Files==
'''/home/PROGRAMS/XPLOR_FILES/analysis'''
==RMS Deviations from Experimental Distance Restraints==
# NOE.cor file needs to be subdivided into separate files containing different constraints classes
## interresidue sequential NOEs (|i-j|=1)
### use awk script: seq_sel.awk '''awk -f seq_sel.awk NOE.cor > seq.cor''' 
### the total number of constraints in the seq.cor file will be listed at the end
## interresidue short range (1 <|i-j| < 5)
### use awk script: short_sel.awk '''awk -f short_sel.awk NOE.cor > short.cor''' 
### the total number of constraints in the short.cor file will be listed at the end
## interresidue long range (1 <|i-j| > 5)
### use awk scrihortpt: long_sel.awk '''awk -f long_sel.awk NOE.cor > long.cor''' 
### the total number of constraints in the long.cor file will be listed at the end
## intraresidue
### use awk script: intra_sel.awk '''awk -f intra_sel.awk NOE.cor > intra.cor''' 
### the total number of constraints in the intra.cor file will be listed at the end
## H-bonds
### These constraints need to be hand collated and counted into the file h-bonds.cor 
### They should all be located in one region (end) of the original NOE.cor file 
# Edit energy.inp and energy_ave.inp to include the filenames for your PSF file, 30 best structures (energy) and restrained minimized structure (energy_ave). 
# Run XPLOR and parse output file:
## '''xplor < energy_ave.inp >& energy.out &'''
## '''csh stat.csh > stat_ave.out'''
## '''cp energy.out energy_ave.out'''
## ''' xplor < energy.inp >& energy.out &'''
## ''' csh stat.csh > stat.out'''
# The files stat.out and stat_ave.out contain the rms deviations from experimental distance restraints for the table.
## A typical stat.out file will looke like: ''RMS_NOE- Column 6 mean: 0.0410533 Std Dev 0.00483168 (N= 30 )'' ''RMS_CDIH- Column 6 mean: 1.43315 Std Dev 0.794072 (N= 30 )'' ''RMS_BONDS (1993)- Column 6 mean: 0.00519457 Std Dev 0.000252635 (N= 30 )'' ''RMS_ANGLES (3655)- Column 6 mean: 0.621244 Std Dev 0.030363 (N= 30 )'' ''RMS_IMPROPERS (972)- Column 6 mean: 0.518672 Std Dev 0.0634619 (N= 30 ) ''RMS_NOE_H-BONDS- Column 7 mean: 0.0958333 Std Dev 0.0133618 (N= 30 )'' ''RMS_NOE_INTRA- Column 7 mean: 0.0075 Std Dev 0.00455887 (N= 30 )'' ''RMS_NOE_LONG- Column 7 mean: 0.0451 Std Dev 0.00898647 (N= 30 )'' ''RMS_NOE_SEQ- Column 7 mean: 0.0378333 Std Dev 0.00800451 (N= 30 )'' ''RMS_NOE_SHORT- Column 7 mean: 0.0427 Std Dev 0.00536128 (N= 30 )'' ''ENERGY_BOND- Column 7 mean: 53.9053 Std Dev 5.35852 (N= 60 )'' ''ENERGY_ANGLE- Column 9 mean: 215.364 Std Dev 21.6272 (N= 60 )'' ''ENERGY_IMPR- Column 5 mean: 40.4231 Std Dev 10.4815 (N= 30 )'' ''ENERGY_REP- Column 8 mean: 107.973 Std Dev 23.6387 (N= 30 )'' ''ENERGY_LJ- Column 8 mean: -374.082 Std Dev 21.1904 (N= 30 )'' ''ENERGY_CDIH- Column 5 mean: 35.9804 Std Dev 45.4492 (N= 30 )'' ''ENERGY_NOE- Column 8 mean: 234.949 Std Dev 57.3573 (N= 30 )''}} 
##rms deviations from experimental distance restraints from the stat.out file
###all ''RMS_NOE- Column 6 mean: 0.0410533 Std Dev 0.00483168 (N= 30 )'' 
###interresidue sequential (|i-j| = 1) ''RMS_NOE_SEQ- Column 7 mean: 0.0378333 Std Dev 0.00800451 (N= 30 )'' 
###interresidue long-range (|i-j| > 5) ''RMS_NOE_LONG- Column 7 mean: 0.0451 Std Dev 0.00898647 (N= 30 )'' 
###Intraresidue ''RMS_NOE_INTRA- Column 7 mean: 0.0075 Std Dev 0.00455887 (N= 30 )'' 
###H-bonds ''RMS_NOE_H-BONDS- Column 7 mean: 0.0958333 Std Dev 0.0133618 (N= 30 )'' 
==RMS Deviation from Experimental Dihedral Restraints (deg)==
# Include the appropriate dihedral contraint (dihed.tbl) file in the energy.inp file used above.
#The value is reported in the stat.out file: ''RMS_CDIH- Column 6 mean: 1.43315 Std Dev 0.794072 (N= 30 )'' 
# To count the number of dihedral restraints used to refine the structure, use the awk script cnt_ang.nawk '''awk –f cnt_ang.nawk dihed.tbl''' 
==RMS Deviation from Experimental Cα Restraints (ppm)==
#Use the CARB_AVE.nawk awk script to parse the ''best'' 30 simulated annealing structures '''awk -f CARB_AVE.nawk *dg*.sam''' 
## *dg*.sam is the wild-card representation of the list of 30 simulated annealing structures
## Please use the proper representation to list your 30 best structures
# Typical output of CARB_AVE.nawk ''Average CA RMS: 0.885654 +/- 0.0299637 For 30 values.'' ''Average CB RMS: 0.905546 +/- 0.0229673 For 30 values.'' ''Average J RMS: 0.606855 +/- 0.04947 For 30 values.'' 
# To count the number of Cα carbon restrains used to refine the structure, us the awk script cnt_ang.nawk '''awk -f cnt_carbon.nawk carbon.tbl 
# This approach can be repeated to determine rms deviation from experimental Cβ restraints (ppm)
==RMS Deviation from 3JNHα Restrains (Hz)==
# Same approach as '''RMS Deviation from Experimental Cα Restraints (ppm)'''
#To count the number of coupling restraints used to refine the structure, use the awk script cnt_coupling.nawk '''awk -f cnt_coupling.nawk coupling.tbl 
==Structure Energies==
# FNOE (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_NOE- Column 8 mean: 234.949 Std Dev 57.3573 (N= 30 )'' 
#Ftor (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_CDIH- Column 5 mean: 35.9804 Std Dev 45.4492 (N= 30 )'' 
#Frepel (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_REP- Column 8 mean: 107.973 Std Dev 23.6387 (N= 30 )'' 
#FL-J (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_LJ- Column 8 mean: -374.082 Std Dev 21.1904 (N= 30 )'' 
==Deviations from Idealized Covalent Geometry==
# bonds (Å)
## The value is reported in the stat.out (see above): ''RMS_BONDS (1993)- Column 6 mean: 0.00519457 Std Dev 0.000252635 (N= 30 )'' 
## The number of bonds is the value in the parenthesis
### 1993 in the example above 
# angles (deg)
## The value is reported in the stat.out file (see above): ''RMS_ANGLES (3655)- Column 6 mean: 0.621244 Std Dev 0.030363 (N= 30 )'' 
## The number of angles is the value in the parenthesis
### 3655 in the example above 
# impropers (deg)
## The value is reported in the stat.out file (see above): ''RMS_IMPROPERS (972)- Column 6 mean: 0.518672 Std Dev 0.0634619 (N= 30 )'' 
## The number of improper dihedral angles is the value in the paranthesis
### 972 in the example 
==PROCHECK==
# Run PROCHECK on each individual structure file from the list of 30 Best Structures '''procheck structure filename 1.0''' 
# Calculate averages and standard deviations using awk script PRO_AVE.nawk '''awk -f PRO_AVE.nawk *dg*.sum''' 
## *dg*sum is the list of procheck output *.sum files for each of the 30 Best Structures
## Make sure the wild-card form only selects for the correct 30 structures
## Typical output: ''Average rama RMS: 83.5167 +/- 2.5297 For 30 values.'' ''Average G-factors RMS: -0.107333 +/- 0.0287441 For 30 values.'' ''Average bad contacts RMS: 17.5 +/- 2.53969 For 30 values.'' 
## Overall G-Factor: ''Average G-factors RMS: -0.107333 +/- 0.0287441 For 30 values.'' 
## %Residues in most favorable region of Ramachandran plot ''Average rama RMS: 83.5167 +/- 2.5297 For 30 values.'' 
## Number of bad contacts/100 residues ''Average bad contacts RMS: 17.5 +/- 2.53969 For 30 values.'' 
### Number needs to be scaled to 100 residues. Multiply by 100/number of residues. 
# Calculate averages and standard deviations using awk script PRO_AVE_2.nawk ''' awk -f PRO_AVE_2.nawk *dg*.out''' 
## *dg*.out is the list of procheck output *.out files for each of the 30 Best Structures
## Make sure the wild-card form only selects for the correct 30 structures
## Typical output: ''Average hbond RMS: 1.04333 +/- 0.0558768 For 30 values.'' 
## The above result is the H-bond energy 
==Atomic RMS Differences==
# Use the rmsdiff.inp and rmsdiff_sec.inp XPLOR scripts
# Repeat the calculates twice, once with the average structure (SA) as the reference structure and the other time with the restrained minimized average structures (SA)r as the reference structure
## Evaluate ($1 = "reference structure name")
# Include the 30 best structures, the average structure and the restrained minimized average structure names in the for loop
# Exclude regions of poorly defined structure in the select statments for both the fit and rms calculations
# Only include regions of α-helix and/or β-sheets in the rmsdiff_sec.inp for both the fit and rms calculations
# Use the awk script average.nawk to calculate the average and standard deviation of the 30 Best Structures '''awk –f average.nawk back_all.rms''' 
## rmsd for backbone atoms
## back_sec.rms output file for rmsdiff_sec.inp file
## Make sure only the 30 Best Structures are list in file
### Need to delete results for average and restrained minimized average structure from back_all.rms
### Make backup first
### Record (SA)r vs SA rmsd values before deleting
### Typical output: ''Average RMS: 0.408533 +/- 0.056732 For 30 values.'' 
# Use average.nawk awk script '''awk –f average.nawk all_all.rms''' 
## rmsd for all atoms
## all_sec.rms output file for rmsdiff_sec.inp file
## Make sure only the 30 Best Structures are listed in file
### Need to delete results for average and restrained minimized average structure
### Make backup first
### Record (SA)r vs SA rmsd values before deleting
### Typical output ''Average RMS: 1.00183 +/- 0.0711051 For 30 values.'' 

==Example Structural Statistics Table==

[[File:Structure_energy_table.doc]]

Generating Protein Structure Statistics Table

2013-12-15T16:58:41Z

Wiki Administrator: /* Experimental: Python table calculator */

[[Media:Example.ogg]][[category:Protocols]]
==Definitions==
# <SA> is an ensemble of the "best" 30 simulated annealing structures
# SA is average structure
# (SA)r is the restrained minimized average structures
= Experimental: Python table calculator =
Run the following commands if you want to try the automagic structure statistics table calculator:

cp /home/bworley/research/struct-stats/*.{py,inp.in} ./
vi options.py
./Table.py
cat table.txt

The step in which '''options.py''' is edited is the most critical. All the files required by the calculator must be available in the current working directory and accessible by the filenames stored in the options file.

Use at your own risk. If it doesn't work, it doesn't work. If it does work, it will complete all tasks described below except the PROCHECK analysis.

==Location of XPLOR, awk and csh Files==
'''/home/PROGRAMS/XPLOR_FILES/analysis'''
==RMS Deviations from Experimental Distance Restraints==
# NOE.cor file needs to be subdivided into separate files containing different constraints classes
## interresidue sequential NOEs (|i-j|=1)
### use awk script: seq_sel.awk '''awk -f seq_sel.awk NOE.cor > seq.cor''' 
### the total number of constraints in the seq.cor file will be listed at the end
## interresidue short range (1 <|i-j| < 5)
### use awk script: short_sel.awk '''awk -f short_sel.awk NOE.cor > short.cor''' 
### the total number of constraints in the short.cor file will be listed at the end
## interresidue long range (1 <|i-j| > 5)
### use awk scrihortpt: long_sel.awk '''awk -f long_sel.awk NOE.cor > long.cor''' 
### the total number of constraints in the long.cor file will be listed at the end
## intraresidue
### use awk script: intra_sel.awk '''awk -f intra_sel.awk NOE.cor > intra.cor''' 
### the total number of constraints in the intra.cor file will be listed at the end
## H-bonds
### These constraints need to be hand collated and counted into the file h-bonds.cor 
### They should all be located in one region (end) of the original NOE.cor file 
# Edit energy.inp and energy_ave.inp to include the filenames for your PSF file, 30 best structures (energy) and restrained minimized structure (energy_ave). 
# Run XPLOR and parse output file:
## '''xplor < energy_ave.inp >& energy.out &'''
## '''csh stat.csh > stat_ave.out'''
## '''cp energy.out energy_ave.out'''
## ''' xplor < energy.inp >& energy.out &'''
## ''' csh stat.csh > stat.out'''
# The files stat.out and stat_ave.out contain the rms deviations from experimental distance restraints for the table.
## A typical stat.out file will looke like: ''RMS_NOE- Column 6 mean: 0.0410533 Std Dev 0.00483168 (N= 30 )'' ''RMS_CDIH- Column 6 mean: 1.43315 Std Dev 0.794072 (N= 30 )'' ''RMS_BONDS (1993)- Column 6 mean: 0.00519457 Std Dev 0.000252635 (N= 30 )'' ''RMS_ANGLES (3655)- Column 6 mean: 0.621244 Std Dev 0.030363 (N= 30 )'' ''RMS_IMPROPERS (972)- Column 6 mean: 0.518672 Std Dev 0.0634619 (N= 30 ) ''RMS_NOE_H-BONDS- Column 7 mean: 0.0958333 Std Dev 0.0133618 (N= 30 )'' ''RMS_NOE_INTRA- Column 7 mean: 0.0075 Std Dev 0.00455887 (N= 30 )'' ''RMS_NOE_LONG- Column 7 mean: 0.0451 Std Dev 0.00898647 (N= 30 )'' ''RMS_NOE_SEQ- Column 7 mean: 0.0378333 Std Dev 0.00800451 (N= 30 )'' ''RMS_NOE_SHORT- Column 7 mean: 0.0427 Std Dev 0.00536128 (N= 30 )'' ''ENERGY_BOND- Column 7 mean: 53.9053 Std Dev 5.35852 (N= 60 )'' ''ENERGY_ANGLE- Column 9 mean: 215.364 Std Dev 21.6272 (N= 60 )'' ''ENERGY_IMPR- Column 5 mean: 40.4231 Std Dev 10.4815 (N= 30 )'' ''ENERGY_REP- Column 8 mean: 107.973 Std Dev 23.6387 (N= 30 )'' ''ENERGY_LJ- Column 8 mean: -374.082 Std Dev 21.1904 (N= 30 )'' ''ENERGY_CDIH- Column 5 mean: 35.9804 Std Dev 45.4492 (N= 30 )'' ''ENERGY_NOE- Column 8 mean: 234.949 Std Dev 57.3573 (N= 30 )''}} 
##rms deviations from experimental distance restraints from the stat.out file
###all ''RMS_NOE- Column 6 mean: 0.0410533 Std Dev 0.00483168 (N= 30 )'' 
###interresidue sequential (|i-j| = 1) ''RMS_NOE_SEQ- Column 7 mean: 0.0378333 Std Dev 0.00800451 (N= 30 )'' 
###interresidue long-range (|i-j| > 5) ''RMS_NOE_LONG- Column 7 mean: 0.0451 Std Dev 0.00898647 (N= 30 )'' 
###Intraresidue ''RMS_NOE_INTRA- Column 7 mean: 0.0075 Std Dev 0.00455887 (N= 30 )'' 
###H-bonds ''RMS_NOE_H-BONDS- Column 7 mean: 0.0958333 Std Dev 0.0133618 (N= 30 )'' 
==RMS Deviation from Experimental Dihedral Restraints (deg)==
# Include the appropriate dihedral contraint (dihed.tbl) file in the energy.inp file used above.
#The value is reported in the stat.out file: ''RMS_CDIH- Column 6 mean: 1.43315 Std Dev 0.794072 (N= 30 )'' 
# To count the number of dihedral restraints used to refine the structure, use the awk script cnt_ang.nawk '''awk –f cnt_ang.nawk dihed.tbl''' 
==RMS Deviation from Experimental Cα Restraints (ppm)==
#Use the CARB_AVE.nawk awk script to parse the ''best'' 30 simulated annealing structures '''awk -f CARB_AVE.nawk *dg*.sam''' 
## *dg*.sam is the wild-card representation of the list of 30 simulated annealing structures
## Please use the proper representation to list your 30 best structures
# Typical output of CARB_AVE.nawk ''Average CA RMS: 0.885654 +/- 0.0299637 For 30 values.'' ''Average CB RMS: 0.905546 +/- 0.0229673 For 30 values.'' ''Average J RMS: 0.606855 +/- 0.04947 For 30 values.'' 
# To count the number of Cα carbon restrains used to refine the structure, us the awk script cnt_ang.nawk '''awk -f cnt_carbon.nawk carbon.tbl 
# This approach can be repeated to determine rms deviation from experimental Cβ restraints (ppm)
==RMS Deviation from 3JNHα Restrains (Hz)==
# Same approach as '''RMS Deviation from Experimental Cα Restraints (ppm)'''
#To count the number of coupling restraints used to refine the structure, use the awk script cnt_coupling.nawk '''awk -f cnt_coupling.nawk coupling.tbl 
==Structure Energies==
# FNOE (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_NOE- Column 8 mean: 234.949 Std Dev 57.3573 (N= 30 )'' 
#Ftor (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_CDIH- Column 5 mean: 35.9804 Std Dev 45.4492 (N= 30 )'' 
#Frepel (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_REP- Column 8 mean: 107.973 Std Dev 23.6387 (N= 30 )'' 
#FL-J (kcal mol-1)
## The value is reported in the stat.out file (see above): ''ENERGY_LJ- Column 8 mean: -374.082 Std Dev 21.1904 (N= 30 )'' 
==Deviations from Idealized Covalent Geometry==
# bonds (Å)
## The value is reported in the stat.out (see above): ''RMS_BONDS (1993)- Column 6 mean: 0.00519457 Std Dev 0.000252635 (N= 30 )'' 
## The number of bonds is the value in the parenthesis
### 1993 in the example above 
# angles (deg)
## The value is reported in the stat.out file (see above): ''RMS_ANGLES (3655)- Column 6 mean: 0.621244 Std Dev 0.030363 (N= 30 )'' 
## The number of angles is the value in the parenthesis
### 3655 in the example above 
# impropers (deg)
## The value is reported in the stat.out file (see above): ''RMS_IMPROPERS (972)- Column 6 mean: 0.518672 Std Dev 0.0634619 (N= 30 )'' 
## The number of improper dihedral angles is the value in the paranthesis
### 972 in the example 
==PROCHECK==
# Run PROCHECK on each individual structure file from the list of 30 Best Structures '''procheck structure filename 1.0''' 
# Calculate averages and standard deviations using awk script PRO_AVE.nawk '''awk -f PRO_AVE.nawk *dg*.sum''' 
## *dg*sum is the list of procheck output *.sum files for each of the 30 Best Structures
## Make sure the wild-card form only selects for the correct 30 structures
## Typical output: ''Average rama RMS: 83.5167 +/- 2.5297 For 30 values.'' ''Average G-factors RMS: -0.107333 +/- 0.0287441 For 30 values.'' ''Average bad contacts RMS: 17.5 +/- 2.53969 For 30 values.'' 
## Overall G-Factor: ''Average G-factors RMS: -0.107333 +/- 0.0287441 For 30 values.'' 
## %Residues in most favorable region of Ramachandran plot ''Average rama RMS: 83.5167 +/- 2.5297 For 30 values.'' 
## Number of bad contacts/100 residues ''Average bad contacts RMS: 17.5 +/- 2.53969 For 30 values.'' 
### Number needs to be scaled to 100 residues. Multiply by 100/number of residues. 
# Calculate averages and standard deviations using awk script PRO_AVE_2.nawk ''' awk -f PRO_AVE_2.nawk *dg*.out''' 
## *dg*.out is the list of procheck output *.out files for each of the 30 Best Structures
## Make sure the wild-card form only selects for the correct 30 structures
## Typical output: ''Average hbond RMS: 1.04333 +/- 0.0558768 For 30 values.'' 
## The above result is the H-bond energy 
==Atomic RMS Differences==
# Use the rmsdiff.inp and rmsdiff_sec.inp XPLOR scripts
# Repeat the calculates twice, once with the average structure (SA) as the reference structure and the other time with the restrained minimized average structures (SA)r as the reference structure
## Evaluate ($1 = "reference structure name")
# Include the 30 best structures, the average structure and the restrained minimized average structure names in the for loop
# Exclude regions of poorly defined structure in the select statments for both the fit and rms calculations
# Only include regions of α-helix and/or β-sheets in the rmsdiff_sec.inp for both the fit and rms calculations
# Use the awk script average.nawk to calculate the average and standard deviation of the 30 Best Structures '''awk –f average.nawk back_all.rms''' 
## rmsd for backbone atoms
## back_sec.rms output file for rmsdiff_sec.inp file
## Make sure only the 30 Best Structures are list in file
### Need to delete results for average and restrained minimized average structure from back_all.rms
### Make backup first
### Record (SA)r vs SA rmsd values before deleting
### Typical output: ''Average RMS: 0.408533 +/- 0.056732 For 30 values.'' 
# Use average.nawk awk script '''awk –f average.nawk all_all.rms''' 
## rmsd for all atoms
## all_sec.rms output file for rmsdiff_sec.inp file
## Make sure only the 30 Best Structures are listed in file
### Need to delete results for average and restrained minimized average structure
### Make backup first
### Record (SA)r vs SA rmsd values before deleting
### Typical output ''Average RMS: 1.00183 +/- 0.0711051 For 30 values.'' 

==Example Structural Statistics Table==

[[File:Structure_energy_table.doc]]

Cluster Maintenance

2013-10-22T00:23:56Z

Wiki Administrator: /* DHCP */

= Hardware =
The cluster was built from parts ordered from [http://www.newegg.com Newegg]. The important components of the system are as follows:

* '''PSU:''' ''(1x)'' Corsair RM850 850W 92% Efficiency Active-PFC
* '''Mobo:''' ''(1x)'' Gigabyte GA-EP45-UD3P (rev 1.1)
* '''CPU:''' ''(1x)'' Intel Core 2 Quad Q8300 2.5GHz
* '''RAM:''' ''(4x)'' Corsair XMS2 DDR2 800 (PC2 6400) 2GB
* '''Gfx:''' ''(1x)'' NVIDIA GeForce 9500 GT PCI-E 2.0 x8
* '''RAID:''' ''(1x)'' 3ware 9650SE-4LMPL PCI-E 2.0 x1
* '''RAID:''' ''(4x)'' WD 1TB 7200RPM SATA-II HDD

= Operating System =
The cluster currently runs Debian 7.0 ''amd64''. The recommended method of installing the base operating system is to download the ''Small CD'' ISO from [http://www.debian.org/distrib/netinst Debian] and burn it to a CD/DVD.

The (MBR) partitioning of the main 1TB disk should be:

{|
| Num. || Size || Filesystem || Mount point
|-
| 1 || 256 MB || ext2 || /boot
|-
| 2 || 317 GB || ext4 || /
|-
| 3 || 2.5 GB || swap || swap
|}

The 2.7TB RAID5 array should ''already be partitioned'' (GPT). '''At all costs, maintain the integrity of the data already contained on the RAID5 array.''' Keep frequent backups of the array to at least one external source.

Other important settings to choose during the installation are summarized below:
FIXME

= Software =
The software on the cluster consists of packages installed through the Debian repositories and third-party software installed into '''/opt'''. It is highly recommended that the software in this section be installed in the order it is listed here, if possible.

== Debian Packages ==
Install Debian packages before third-party software, if at all possible. Many of these commands will require mounting the administrator flash drive, in which case this documentation assumes it will be mounted to '''/mnt/flash'''.

=== Initial configuration ===
We don't want all the ports on our precious cluster to be out there flapping in the breeze. Install some files that loosely restrict which daemons can provide services to which addresses:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/hosts.allow /etc/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/hosts.deny /etc/

Install a file that defines WAN and LAN IP-hostname mappings:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/hosts /etc/

Add support for hosting both 32-bit and 64-bit packages on this 64-bit system:

dpkg --add-architecture i386
apt-get update

Now install the the following packages using ''apt-get'':

* libc6-i686
* libx11-6:i386
* libxext6:i386

=== The groundwork ===
Some miscellaneous software packages need to be installed as boilerplate. Install the following packages using ''apt-get''...

First, install some required shells:

* tcsh
* bash-completion

Lay down a decent text editor:

* vim

Add a few extra utilities:

* zip
* nmap
* links
* rsync
* screen
* gnuplot
* imagemagick

Now install some more language support:

* pkg-config
* build-essential
* libtool
* texlive
* texi2html
* ruby
* gfortran
* perl

=== Python ===
A few Python packages are standard fare for programmers in the group. Install the following packages using ''apt-get'':

* python3
* python2.7
* python3.2
* python-numpy
* python-sklearn
* python-matplotlib

=== R ===
The R language is useful to some people, I guess.

* r-base
* r-recommended

=== Sudo ===
Install the ''sudo'' package using ''apt-get''. Then add the following line to the '''/etc/sudoers''' file:

%bionmr ALL=(ALL:ALL) ALL

=== OpenSSH ===
The OpenSSH daemon allows users to log into the cluster from anywhere in the world using their RSA private key. First, install the following packages using ''apt-get'':

* openssh-client
* openssh-server

Then install the '''/etc/ssh/sshd_config''' file from the administrator flash drive and restart the SSH daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/ssh/sshd_config /etc/ssh/
service ssh restart

=== NFS ===
The NFS server allows users to access their files on campus from Debian Linux workstations. First, install the following packages using ''apt-get'':

* nfs-kernel-server
* portmap

Then install the '''/etc/exports''' file from the administrator flash drive and restart the NFS daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/exports /etc/
service nfs-kernel-server restart

=== Samba ===
The Samba server allows users to access their files on campus from Windows workstations. First, install the following packages using ''apt-get'':

* cifs-utils
* samba

Then install the Samba configuration and password files and restart the Samba daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/samba/smb.conf /etc/samba/
install -v -m 600 -o root -g root /mnt/flash/admin-tools/linux/cluster/var/lib/samba/passdb.tdb /var/lib/samba/
service samba restart

=== MySQL ===
FIXME

* mysql-client
* mysql-server

=== Apache ===
The Apache server hosts the group website, plain and simple. Install the following packages using ''apt-get'':

* apache2
* apache2-doc

Then install the password file and an updated site configuration file and restart the Apache daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/apache2/htpasswd /etc/apache2/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/apache2/sites-available/default /etc/apache2/sites-available
service apache2 restart

=== PHP ===
The PHP interpreter is required to host the website using the UNL university style templates. Install the following packages using ''apt-get'':

* php5
* php5-mysql
* php5-sqlite
* libapache-mod-php5

Then download and install Pyrus (PEAR2) using the following commands:

wget http://pear2.php.net/pyrus.phar
install -v -m 644 -o root -g root pyrus.phar /usr/bin/
rm pyrus.phar

Open a new file in ''vi'' called '''/usr/bin/pyrus''' and add the following text:

#!/bin/bash
/usr/bin/php -dphar.readonly=0 /usr/bin/pyrus.phar $*

Save the file and make it executable:

chmod 755 /usr/bin/pyrus

Now run ''pyrus'' for the first time. Tell it ''yes'' to initialize the configuration. Tell it to install packages to '''/usr/share/pear''' by default, when it asks. Now install the UNL template package:

pyrus channel-discover pear.unl.edu
pyrus install -o pear.unl.edu/UNL_Templates-beta

Finally, install updated configuration files for PHP, restart the Apache server and remove the placeholder html page:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/php5/apache2/php.ini /etc/php5/apache2/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/php5/cli/php.ini /etc/php5/cli/
service apache2 restart
rm /var/www/index.html

=== DHCP ===
The cluster LAN is managed by a DHCP server on the second Ethernet port. Install the following package using ''apt-get'':

* isc-dhcp-server
* bridge-utils
* dnsmasq

Install the configuration files for the DHCP server:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/dhcp/dhcpd.conf /etc/dhcp/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/default/isc-dhcp-server /etc/default/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/network/interfaces /etc/network/

Bring up the second Ethernet interface and restart the DHCP server:

ifup eth1
service isc-dhcp-server restart

Run the following commands:

brctl addbr br0
brctl addif br0 eth0 eth1
ifup br0

=== Octave ===
The Octave programming environment provides users with mathematical routines that simplify data handling. Install the following packages using ''apt-get'':

* octave
* liboctave-dev
* octave-audio
* octave-control
* octave-data-smoothing
* octave-fixed
* octave-fpl
* octave-general
* octave-geometry
* octave-image
* octave-io
* octave-linear-algebra
* octave-odepkg
* octave-optim
* octave-optiminterp
* octave-pkg-dev
* octave-plot
* octave-quaternion
* octave-signal
* octave-specfun
* octave-statistics
* octave-strings

== Third-party Software ==
FIXME

[[Category:Sysadmin]]

Cluster Maintenance

2013-10-21T23:29:31Z

Wiki Administrator: /* DHCP */

= Hardware =
The cluster was built from parts ordered from [http://www.newegg.com Newegg]. The important components of the system are as follows:

* '''PSU:''' ''(1x)'' Corsair RM850 850W 92% Efficiency Active-PFC
* '''Mobo:''' ''(1x)'' Gigabyte GA-EP45-UD3P (rev 1.1)
* '''CPU:''' ''(1x)'' Intel Core 2 Quad Q8300 2.5GHz
* '''RAM:''' ''(4x)'' Corsair XMS2 DDR2 800 (PC2 6400) 2GB
* '''Gfx:''' ''(1x)'' NVIDIA GeForce 9500 GT PCI-E 2.0 x8
* '''RAID:''' ''(1x)'' 3ware 9650SE-4LMPL PCI-E 2.0 x1
* '''RAID:''' ''(4x)'' WD 1TB 7200RPM SATA-II HDD

= Operating System =
The cluster currently runs Debian 7.0 ''amd64''. The recommended method of installing the base operating system is to download the ''Small CD'' ISO from [http://www.debian.org/distrib/netinst Debian] and burn it to a CD/DVD.

The (MBR) partitioning of the main 1TB disk should be:

{|
| Num. || Size || Filesystem || Mount point
|-
| 1 || 256 MB || ext2 || /boot
|-
| 2 || 317 GB || ext4 || /
|-
| 3 || 2.5 GB || swap || swap
|}

The 2.7TB RAID5 array should ''already be partitioned'' (GPT). '''At all costs, maintain the integrity of the data already contained on the RAID5 array.''' Keep frequent backups of the array to at least one external source.

Other important settings to choose during the installation are summarized below:
FIXME

= Software =
The software on the cluster consists of packages installed through the Debian repositories and third-party software installed into '''/opt'''. It is highly recommended that the software in this section be installed in the order it is listed here, if possible.

== Debian Packages ==
Install Debian packages before third-party software, if at all possible. Many of these commands will require mounting the administrator flash drive, in which case this documentation assumes it will be mounted to '''/mnt/flash'''.

=== Initial configuration ===
We don't want all the ports on our precious cluster to be out there flapping in the breeze. Install some files that loosely restrict which daemons can provide services to which addresses:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/hosts.allow /etc/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/hosts.deny /etc/

Install a file that defines WAN and LAN IP-hostname mappings:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/hosts /etc/

Add support for hosting both 32-bit and 64-bit packages on this 64-bit system:

dpkg --add-architecture i386
apt-get update

Now install the the following packages using ''apt-get'':

* libc6-i686
* libx11-6:i386
* libxext6:i386

=== The groundwork ===
Some miscellaneous software packages need to be installed as boilerplate. Install the following packages using ''apt-get''...

First, install some required shells:

* tcsh
* bash-completion

Lay down a decent text editor:

* vim

Add a few extra utilities:

* zip
* nmap
* links
* rsync
* screen
* gnuplot
* imagemagick

Now install some more language support:

* pkg-config
* build-essential
* libtool
* texlive
* texi2html
* ruby
* gfortran
* perl

=== Python ===
A few Python packages are standard fare for programmers in the group. Install the following packages using ''apt-get'':

* python3
* python2.7
* python3.2
* python-numpy
* python-sklearn
* python-matplotlib

=== R ===
The R language is useful to some people, I guess.

* r-base
* r-recommended

=== Sudo ===
Install the ''sudo'' package using ''apt-get''. Then add the following line to the '''/etc/sudoers''' file:

%bionmr ALL=(ALL:ALL) ALL

=== OpenSSH ===
The OpenSSH daemon allows users to log into the cluster from anywhere in the world using their RSA private key. First, install the following packages using ''apt-get'':

* openssh-client
* openssh-server

Then install the '''/etc/ssh/sshd_config''' file from the administrator flash drive and restart the SSH daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/ssh/sshd_config /etc/ssh/
service ssh restart

=== NFS ===
The NFS server allows users to access their files on campus from Debian Linux workstations. First, install the following packages using ''apt-get'':

* nfs-kernel-server
* portmap

Then install the '''/etc/exports''' file from the administrator flash drive and restart the NFS daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/exports /etc/
service nfs-kernel-server restart

=== Samba ===
The Samba server allows users to access their files on campus from Windows workstations. First, install the following packages using ''apt-get'':

* cifs-utils
* samba

Then install the Samba configuration and password files and restart the Samba daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/samba/smb.conf /etc/samba/
install -v -m 600 -o root -g root /mnt/flash/admin-tools/linux/cluster/var/lib/samba/passdb.tdb /var/lib/samba/
service samba restart

=== MySQL ===
FIXME

* mysql-client
* mysql-server

=== Apache ===
The Apache server hosts the group website, plain and simple. Install the following packages using ''apt-get'':

* apache2
* apache2-doc

Then install the password file and an updated site configuration file and restart the Apache daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/apache2/htpasswd /etc/apache2/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/apache2/sites-available/default /etc/apache2/sites-available
service apache2 restart

=== PHP ===
The PHP interpreter is required to host the website using the UNL university style templates. Install the following packages using ''apt-get'':

* php5
* php5-mysql
* php5-sqlite
* libapache-mod-php5

Then download and install Pyrus (PEAR2) using the following commands:

wget http://pear2.php.net/pyrus.phar
install -v -m 644 -o root -g root pyrus.phar /usr/bin/
rm pyrus.phar

Open a new file in ''vi'' called '''/usr/bin/pyrus''' and add the following text:

#!/bin/bash
/usr/bin/php -dphar.readonly=0 /usr/bin/pyrus.phar $*

Save the file and make it executable:

chmod 755 /usr/bin/pyrus

Now run ''pyrus'' for the first time. Tell it ''yes'' to initialize the configuration. Tell it to install packages to '''/usr/share/pear''' by default, when it asks. Now install the UNL template package:

pyrus channel-discover pear.unl.edu
pyrus install -o pear.unl.edu/UNL_Templates-beta

Finally, install updated configuration files for PHP, restart the Apache server and remove the placeholder html page:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/php5/apache2/php.ini /etc/php5/apache2/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/php5/cli/php.ini /etc/php5/cli/
service apache2 restart
rm /var/www/index.html

=== DHCP ===
The cluster LAN is managed by a DHCP server on the second Ethernet port. Install the following package using ''apt-get'':

* isc-dhcp-server

Install the configuration files for the DHCP server:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/dhcp/dhcpd.conf /etc/dhcp/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/default/isc-dhcp-server /etc/default/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/network/interfaces /etc/network/

Bring up the second Ethernet interface and restart the DHCP server:

ifup eth1
service isc-dhcp-server restart

Install the following package using ''apt-get'':

* bridge-utils

Run the following commands:

brctl addbr br0
brctl addif br0 eth0 eth1
ifup br0

=== Octave ===
The Octave programming environment provides users with mathematical routines that simplify data handling. Install the following packages using ''apt-get'':

* octave
* liboctave-dev
* octave-audio
* octave-control
* octave-data-smoothing
* octave-fixed
* octave-fpl
* octave-general
* octave-geometry
* octave-image
* octave-io
* octave-linear-algebra
* octave-odepkg
* octave-optim
* octave-optiminterp
* octave-pkg-dev
* octave-plot
* octave-quaternion
* octave-signal
* octave-specfun
* octave-statistics
* octave-strings

== Third-party Software ==
FIXME

[[Category:Sysadmin]]

Cluster Maintenance

2013-10-04T14:35:50Z

Wiki Administrator:

= Hardware =
The cluster was built from parts ordered from [http://www.newegg.com Newegg]. The important components of the system are as follows:

* '''PSU:''' ''(1x)'' Corsair RM850 850W 92% Efficiency Active-PFC
* '''Mobo:''' ''(1x)'' Gigabyte GA-EP45-UD3P (rev 1.1)
* '''CPU:''' ''(1x)'' Intel Core 2 Quad Q8300 2.5GHz
* '''RAM:''' ''(4x)'' Corsair XMS2 DDR2 800 (PC2 6400) 2GB
* '''Gfx:''' ''(1x)'' NVIDIA GeForce 9500 GT PCI-E 2.0 x8
* '''RAID:''' ''(1x)'' 3ware 9650SE-4LMPL PCI-E 2.0 x1
* '''RAID:''' ''(4x)'' WD 1TB 7200RPM SATA-II HDD

= Operating System =
The cluster currently runs Debian 7.0 ''amd64''. The recommended method of installing the base operating system is to download the ''Small CD'' ISO from [http://www.debian.org/distrib/netinst Debian] and burn it to a CD/DVD.

The (MBR) partitioning of the main 1TB disk should be:

{|
| Num. || Size || Filesystem || Mount point
|-
| 1 || 256 MB || ext2 || /boot
|-
| 2 || 317 GB || ext4 || /
|-
| 3 || 2.5 GB || swap || swap
|}

The 2.7TB RAID5 array should ''already be partitioned'' (GPT). '''At all costs, maintain the integrity of the data already contained on the RAID5 array.''' Keep frequent backups of the array to at least one external source.

Other important settings to choose during the installation are summarized below:
FIXME

= Software =
The software on the cluster consists of packages installed through the Debian repositories and third-party software installed into '''/opt'''. It is highly recommended that the software in this section be installed in the order it is listed here, if possible.

== Debian Packages ==
Install Debian packages before third-party software, if at all possible. Many of these commands will require mounting the administrator flash drive, in which case this documentation assumes it will be mounted to '''/mnt/flash'''.

=== Initial configuration ===
We don't want all the ports on our precious cluster to be out there flapping in the breeze. Install some files that loosely restrict which daemons can provide services to which addresses:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/hosts.allow /etc/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/hosts.deny /etc/

Install a file that defines WAN and LAN IP-hostname mappings:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/hosts /etc/

Add support for hosting both 32-bit and 64-bit packages on this 64-bit system:

dpkg --add-architecture i386
apt-get update

Now install the the following packages using ''apt-get'':

* libc6-i686
* libx11-6:i386
* libxext6:i386

=== The groundwork ===
Some miscellaneous software packages need to be installed as boilerplate. Install the following packages using ''apt-get''...

First, install some required shells:

* tcsh
* bash-completion

Lay down a decent text editor:

* vim

Add a few extra utilities:

* zip
* nmap
* links
* rsync
* screen
* gnuplot
* imagemagick

Now install some more language support:

* pkg-config
* build-essential
* libtool
* texlive
* texi2html
* ruby
* gfortran
* perl

=== Python ===
A few Python packages are standard fare for programmers in the group. Install the following packages using ''apt-get'':

* python3
* python2.7
* python3.2
* python-numpy
* python-sklearn
* python-matplotlib

=== R ===
The R language is useful to some people, I guess.

* r-base
* r-recommended

=== Sudo ===
Install the ''sudo'' package using ''apt-get''. Then add the following line to the '''/etc/sudoers''' file:

%bionmr ALL=(ALL:ALL) ALL

=== OpenSSH ===
The OpenSSH daemon allows users to log into the cluster from anywhere in the world using their RSA private key. First, install the following packages using ''apt-get'':

* openssh-client
* openssh-server

Then install the '''/etc/ssh/sshd_config''' file from the administrator flash drive and restart the SSH daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/ssh/sshd_config /etc/ssh/
service ssh restart

=== NFS ===
The NFS server allows users to access their files on campus from Debian Linux workstations. First, install the following packages using ''apt-get'':

* nfs-kernel-server
* portmap

Then install the '''/etc/exports''' file from the administrator flash drive and restart the NFS daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/exports /etc/
service nfs-kernel-server restart

=== Samba ===
The Samba server allows users to access their files on campus from Windows workstations. First, install the following packages using ''apt-get'':

* cifs-utils
* samba

Then install the Samba configuration and password files and restart the Samba daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/samba/smb.conf /etc/samba/
install -v -m 600 -o root -g root /mnt/flash/admin-tools/linux/cluster/var/lib/samba/passdb.tdb /var/lib/samba/
service samba restart

=== MySQL ===
FIXME

* mysql-client
* mysql-server

=== Apache ===
The Apache server hosts the group website, plain and simple. Install the following packages using ''apt-get'':

* apache2
* apache2-doc

Then install the password file and an updated site configuration file and restart the Apache daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/apache2/htpasswd /etc/apache2/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/apache2/sites-available/default /etc/apache2/sites-available
service apache2 restart

=== PHP ===
The PHP interpreter is required to host the website using the UNL university style templates. Install the following packages using ''apt-get'':

* php5
* php5-mysql
* php5-sqlite
* libapache-mod-php5

Then download and install Pyrus (PEAR2) using the following commands:

wget http://pear2.php.net/pyrus.phar
install -v -m 644 -o root -g root pyrus.phar /usr/bin/
rm pyrus.phar

Open a new file in ''vi'' called '''/usr/bin/pyrus''' and add the following text:

#!/bin/bash
/usr/bin/php -dphar.readonly=0 /usr/bin/pyrus.phar $*

Save the file and make it executable:

chmod 755 /usr/bin/pyrus

Now run ''pyrus'' for the first time. Tell it ''yes'' to initialize the configuration. Tell it to install packages to '''/usr/share/pear''' by default, when it asks. Now install the UNL template package:

pyrus channel-discover pear.unl.edu
pyrus install -o pear.unl.edu/UNL_Templates-beta

Finally, install updated configuration files for PHP, restart the Apache server and remove the placeholder html page:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/php5/apache2/php.ini /etc/php5/apache2/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/php5/cli/php.ini /etc/php5/cli/
service apache2 restart
rm /var/www/index.html

=== DHCP ===
The cluster LAN is managed by a DHCP server on the second Ethernet port. Install the following package using ''apt-get'':

* isc-dhcp-server

Install the configuration files for the DHCP server:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/dhcp/dhcpd.conf /etc/dhcp/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/default/isc-dhcp-server /etc/default/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/network/interfaces /etc/network/

Bring up the second Ethernet interface and restart the DHCP server:

ifup eth1
service isc-dhcp-server restart

=== Octave ===
The Octave programming environment provides users with mathematical routines that simplify data handling. Install the following packages using ''apt-get'':

* octave
* liboctave-dev
* octave-audio
* octave-control
* octave-data-smoothing
* octave-fixed
* octave-fpl
* octave-general
* octave-geometry
* octave-image
* octave-io
* octave-linear-algebra
* octave-odepkg
* octave-optim
* octave-optiminterp
* octave-pkg-dev
* octave-plot
* octave-quaternion
* octave-signal
* octave-specfun
* octave-statistics
* octave-strings

== Third-party Software ==
FIXME

[[Category:Sysadmin]]

Cluster Maintenance

2013-10-04T14:35:31Z

Wiki Administrator: Created page with "= Hardware = The cluster was built from parts ordered from [http://www.newegg.com Newegg]. The important components of the system are as follows: * '''PSU:''' ''(1x)'' Corsai..."

= Hardware =
The cluster was built from parts ordered from [http://www.newegg.com Newegg]. The important components of the system are as follows:

* '''PSU:''' ''(1x)'' Corsair RM850 850W 92% Efficiency Active-PFC
* '''Mobo:''' ''(1x)'' Gigabyte GA-EP45-UD3P (rev 1.1)
* '''CPU:''' ''(1x)'' Intel Core 2 Quad Q8300 2.5GHz
* '''RAM:''' ''(4x)'' Corsair XMS2 DDR2 800 (PC2 6400) 2GB
* '''Gfx:''' ''(1x)'' NVIDIA GeForce 9500 GT PCI-E 2.0 x8
* '''RAID:''' ''(1x)'' 3ware 9650SE-4LMPL PCI-E 2.0 x1
* '''RAID:''' ''(4x)'' WD 1TB 7200RPM SATA-II HDD

= Operating System =
The cluster currently runs Debian 7.0 ''amd64''. The recommended method of installing the base operating system is to download the ''Small CD'' ISO from [http://www.debian.org/distrib/netinst Debian] and burn it to a CD/DVD.

The (MBR) partitioning of the main 1TB disk should be:

{|
| Num. || Size || Filesystem || Mount point
|-
| 1 || 256 MB || ext2 || /boot
|-
| 2 || 317 GB || ext4 || /
|-
| 3 || 2.5 GB || swap || swap
|}

The 2.7TB RAID5 array should ''already be partitioned'' (GPT). '''At all costs, maintain the integrity of the data already contained on the RAID5 array.''' Keep frequent backups of the array to at least one external source.

Other important settings to choose during the installation are summarized below:
FIXME

= Software =
The software on the cluster consists of packages installed through the Debian repositories and third-party software installed into '''/opt'''. It is highly recommended that the software in this section be installed in the order it is listed here, if possible.

== Debian Packages ==
Install Debian packages before third-party software, if at all possible. Many of these commands will require mounting the administrator flash drive, in which case this documentation assumes it will be mounted to '''/mnt/flash'''.

=== Initial configuration ===
We don't want all the ports on our precious cluster to be out there flapping in the breeze. Install some files that loosely restrict which daemons can provide services to which addresses:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/hosts.allow /etc/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/hosts.deny /etc/

Install a file that defines WAN and LAN IP-hostname mappings:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/hosts /etc/

Add support for hosting both 32-bit and 64-bit packages on this 64-bit system:

dpkg --add-architecture i386
apt-get update

Now install the the following packages using ''apt-get'':

* libc6-i686
* libx11-6:i386
* libxext6:i386

=== The groundwork ===
Some miscellaneous software packages need to be installed as boilerplate. Install the following packages using ''apt-get''...

First, install some required shells:

* tcsh
* bash-completion

Lay down a decent text editor:

* vim

Add a few extra utilities:

* zip
* nmap
* links
* rsync
* screen
* gnuplot
* imagemagick

Now install some more language support:

* pkg-config
* build-essential
* libtool
* texlive
* texi2html
* ruby
* gfortran
* perl

=== Python ===
A few Python packages are standard fare for programmers in the group. Install the following packages using ''apt-get'':

* python3
* python2.7
* python3.2
* python-numpy
* python-sklearn
* python-matplotlib

=== R ===
The R language is useful to some people, I guess.

* r-base
* r-recommended

=== Sudo ===
Install the ''sudo'' package using ''apt-get''. Then add the following line to the '''/etc/sudoers''' file:

%bionmr ALL=(ALL:ALL) ALL

=== OpenSSH ===
The OpenSSH daemon allows users to log into the cluster from anywhere in the world using their RSA private key. First, install the following packages using ''apt-get'':

* openssh-client
* openssh-server

Then install the '''/etc/ssh/sshd_config''' file from the administrator flash drive and restart the SSH daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/ssh/sshd_config /etc/ssh/
service ssh restart

=== NFS ===
The NFS server allows users to access their files on campus from Debian Linux workstations. First, install the following packages using ''apt-get'':

* nfs-kernel-server
* portmap

Then install the '''/etc/exports''' file from the administrator flash drive and restart the NFS daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/exports /etc/
service nfs-kernel-server restart

=== Samba ===
The Samba server allows users to access their files on campus from Windows workstations. First, install the following packages using ''apt-get'':

* cifs-utils
* samba

Then install the Samba configuration and password files and restart the Samba daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/samba/smb.conf /etc/samba/
install -v -m 600 -o root -g root /mnt/flash/admin-tools/linux/cluster/var/lib/samba/passdb.tdb /var/lib/samba/
service samba restart

=== MySQL ===
FIXME

* mysql-client
* mysql-server

=== Apache ===
The Apache server hosts the group website, plain and simple. Install the following packages using ''apt-get'':

* apache2
* apache2-doc

Then install the password file and an updated site configuration file and restart the Apache daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/apache2/htpasswd /etc/apache2/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/apache2/sites-available/default /etc/apache2/sites-available
service apache2 restart

=== PHP ===
The PHP interpreter is required to host the website using the UNL university style templates. Install the following packages using ''apt-get'':

* php5
* php5-mysql
* php5-sqlite
* libapache-mod-php5

Then download and install Pyrus (PEAR2) using the following commands:

wget http://pear2.php.net/pyrus.phar
install -v -m 644 -o root -g root pyrus.phar /usr/bin/
rm pyrus.phar

Open a new file in ''vi'' called '''/usr/bin/pyrus''' and add the following text:

#!/bin/bash
/usr/bin/php -dphar.readonly=0 /usr/bin/pyrus.phar $*

Save the file and make it executable:

chmod 755 /usr/bin/pyrus

Now run ''pyrus'' for the first time. Tell it ''yes'' to initialize the configuration. Tell it to install packages to '''/usr/share/pear''' by default, when it asks. Now install the UNL template package:

pyrus channel-discover pear.unl.edu
pyrus install -o pear.unl.edu/UNL_Templates-beta

Finally, install updated configuration files for PHP, restart the Apache server and remove the placeholder html page:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/php5/apache2/php.ini /etc/php5/apache2/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/php5/cli/php.ini /etc/php5/cli/
service apache2 restart
rm /var/www/index.html

=== DHCP ===
The cluster LAN is managed by a DHCP server on the second Ethernet port. Install the following package using ''apt-get'':

* isc-dhcp-server

Install the configuration files for the DHCP server:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/dhcp/dhcpd.conf /etc/dhcp/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/default/isc-dhcp-server /etc/default/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/network/interfaces /etc/network/

Bring up the second Ethernet interface and restart the DHCP server:

ifup eth1
service isc-dhcp-server restart

=== Octave ===
The Octave programming environment provides users with mathematical routines that simplify data handling. Install the following packages using ''apt-get'':

* octave
* liboctave-dev
* octave-audio
* octave-control
* octave-data-smoothing
* octave-fixed
* octave-fpl
* octave-general
* octave-geometry
* octave-image
* octave-io
* octave-linear-algebra
* octave-odepkg
* octave-optim
* octave-optiminterp
* octave-pkg-dev
* octave-plot
* octave-quaternion
* octave-signal
* octave-specfun
* octave-statistics
* octave-strings

== Third-party Software ==
FIXME

OpenEye Software

2013-10-04T14:27:37Z

Wiki Administrator:

This page describes the maintenance and use of the various programs for the OpenEye software suite on your workstation and the cluster.

==Installing OpenEye Packages==
'''You must be root to perform these updates! Doing so under any other user account will break the installation.'''

Every two years, the OpenEye software license expires, forcing the user to acquire a new license and reinstall the packages. First, create an account at eyesopen.com and submit your new license file. Then, proceed to the downloads page and download the following (x86_64, RHEL5) tarballs to somewhere on /DATA which will be referred to as ''$pkgdir'':

* babel
* brood
* eon
* filter
* fred
* lexichem
* ogham
* omega
* quacpac
* rocs
* szybki
* vida

Now, ''ssh'' into bionmr-c1 and ''su'' to root, then '''carefully''' perform the following commands:

cd /home/PROGRAMS/OpenEyeBundle
rm -rf openeye-old
mv -f openeye openeye-old
tar xzf ''${pkgdir}''/babel-*.tar.gz
tar xzf ''${pkgdir}''/brood-*.tar.gz
tar xzf ''${pkgdir}''/eon-*.tar.gz
tar xzf ''${pkgdir}''/filter-*.tar.gz
tar xzf ''${pkgdir}''/fred-*.tar.gz
tar xzf ''${pkgdir}''/lexichem-*.tar.gz
tar xzf ''${pkgdir}''/ogham-*.tar.gz
tar xzf ''${pkgdir}''/omega-*.tar.gz
tar xzf ''${pkgdir}''/quacpac-*.tar.gz
tar xzf ''${pkgdir}''/rocs-*.tar.gz
tar xzf ''${pkgdir}''/szybki-*.tar.gz
tar xzf ''${pkgdir}''/vida-*.tar.gz
cp ''${pkgdir}''/oe_license.txt openeye/
chmod 644 openeye/oe_license.txt
chown -R 502:501 openeye

That should do it.

[[category:Protocols]]
[[category:Sysadmin]]
[[category:Molecular Docking]]

PCA Utilities

2013-08-06T17:03:04Z

Wiki Administrator:

The PCA Utilities package provides small software routines for plotting PCA/OPLS scores and building dendrograms based on those scores. This page outlines how to install and use the ''pca-utils'' software.

= Introductions =

== Obtaining ''pca-utils'' ==
You can obtain the source code to ''pca-utils'' by clicking [http://bionmr.unl.edu/pca-utils.php here].

== Installing ''pca-utils'' ==
The PCA utilities are a set of command line open-source UNIX/Linux programs. The software is highly portable: provided your distribution has glibc, it should compile without incident. Once you have the source code, run these commands to install it:

cd /path/to/source/tarball
tar xf pca-utils-YYYYMMDD.tar.gz
cd pca-utils-YYYYMMDD/
make
sudo make install

By default, the programs install to ''/usr/bin'', but you can easily change this by modifying the Makefile if you need to.

== Plotting scores with ellipses ==
[[File:Beatles-plot.png|thumb|right|300px|Example scores plot generated by '''pca-ellipses''']]
For an input list file called ''list.txt'', you can quickly generate a postscript plot file (in this case called ''plot.ps'') that shows your PCA scores with 95% confidence ellipses around each group:

pca-ellipses -1 44.4 -2 22.2 -i ''list.txt'' -k -o ''plot.ps''

In the above statement, the optional arguments ''-1'' and ''-2'' were used to set contributions of PC1 and PC2 to 44.4% and 22.2%, respectively. You can then edit ''plot.ps'' to your liking. If you need a bit more control over your output, you can generate '''gnuplot'''-readable ellipses instead like so:

pca-ellipses -i ''list.txt'' > ellipses.txt
awk -F '\t' '/^[0-9]/{print$3,$4}' ''list.txt'' > points.txt
gnuplot> plot 'points.txt' w p, 'ellipses.txt' w l

Of course, in the second case, you're free to style everything any way you like. Happy hacking!

== Plotting 3D scores with ellipsoids ==
That's right, ladies and gentlemen. You can plot 3D scores! Just use the ''pca-ellipsoids'' command:

pca-ellipsoids -1 44.4 -2 22.2 -3 11.1 -i ''list.txt'' > ''plotscript.plt''

This creates a '''gnuplot'''-syntax script file that you can open up in an interactive gnuplot session like so:

gnuplot
'''gnuplot>''' load 'plotscript.plt'

The above commands will open up a plot window containing the 3D plot, which you can manipulate with the mouse. Once you've found the optimal viewpoint to display the plot, copy the two ''view'' angles at the bottom left corner of the plot window. Then Add the following two lines to the top of the ''plotscript.plt'' file:

set terminal postscript enhanced color
set output 'plot.ps'

Also, change view angles to your values in the following line of the plot script:

set view 60, 35

In other words, change ''60'' and ''35'' to your view angles. Finally, create the postscript file by running '''gnuplot''' again:

gnuplot plotscript.plt

You'll then have a ''plot.ps'' file that can be opened in your favorite graphics editor of choice. Happy editing!

== Generating dendrograms ==
[[File:Beatles-tree.png|thumb|right|300px|Example postscript tree generated by '''pca-bootstrap''']]
Two complementary methods exist for generating trees. The first uses Euclidean distances and bootstrapping statistics, while the second uses Mahalanobis distances and p-values. For datasets containing well-separated groups in scores space, the bootstrapping method will do fine. However, highly separation in overlapped data may be better quantified with p-values in many cases.

=== Using bootstrapping ===
To build a simple tree that displays to the console for quick checks, just run something like this:

pca-bootstrap -i ''list.txt''

The default number of bootstrap iterations is 100, but ''pca-bootstrap'' can easily handle more. You can set the number of iterations to, say 1000, like so:

pca-bootstrap -i ''list.txt'' -n 1000

Everything looks good? You can save a postscript file using the ''-o'' flag:

pca-bootstrap -i ''list.txt'' -n 1000 -k -o ''tree.ps''

=== Using parameterizing ===
To build a simple tree that displays to the console for quick checks, just run something like this:

pca-dendrogram -i ''list.txt''

Everything looks good? You can save a postscript file using the ''-o'' flag:

pca-dendrogram -i ''list.txt'' -k -o ''tree.ps''

If everything works, the plots generated from these methods should look something like this:

+-----------------------------------------------------------George
|3.8e-11
| +-------------------------------------Ringo
+----------------------|1.3e-08
| +-----John
+-----------------------------|0.45
+------Paul

Use of ''pca-bootstrap'' will yield values at the nodes between 0 and 100, while ''pca-dendrogram'' will yield values between 0 and 1.

== Calculating p-values ==
If you just need p-values to accept the null hypothesis, you can use this command:

pca-overlap -i ''list.txt''

== Calculating distances ==
Similar to calculating p-values, raw distances may be extracted using the following command:

pca-distances -i ''list.txt''

Other distance metrics may be supplied using the '''-m''' flag. For example, you can generate a [[wikipedia:Mahalanobis distance|Mahalanobis distance]] matrix like so:

pca-distances -m MAH -i ''list.txt''

== Calculating basic statistics ==
If you're interested in basic information about each group, such as mean and/or covariance, you can use ''pca-stats'':

pca-stats -i ''list.txt''

Goodness, that was easy, wasn't it!?

== Generating random datasets ==
Mainly provided for entertainment value and development/debugging, ''pca-rand'' lets you generate list files that contain bivariate normally distributed point sets. Here's an example command (in the bash scripting language) to build a faux list file:

(pca-rand -H -L John -u '(-2,2)' -v '(2,0.6)' -r 45 -n 10;
pca-rand -L Paul -u '(-2,2)' -v '(2,0.6)' -r 135 -n 9;
pca-rand -L George -u '(3,-2)' -v '(4,3)' -r 120 -n 13;
pca-rand -L Ringo -u '(-1,-1)' -v '(2,2)' -r 0 -n 15) > ''list.txt''

No, you read that right. You can download the list file generated by a single run of this command here: [[File:Beatles.txt]].

= "Wait, I'm still confused" =
Remember that every command in the ''pca-utils'' package has a help message. Just run the command that you need information on with the ''--help'' flag to get a nice message on how to use that command. You can also find manual pages for each command, e.g.:

man pca-dendrogram

[[category:Protocols]]
[[category:Metabolomics]]

Category:Sysadmin

2013-07-25T18:04:39Z

Wiki Administrator:

The Sysadmin category of the wiki provides information that system administrators need to know to do their job. I'll be spending plenty of time adding valuable information to this category as I slowly proceed towards graduation. To the next system administrator of the group: best of luck.

~ Brad.

Installing workstations

2013-07-25T18:03:49Z

Wiki Administrator:

Workstations in the group are 64-bit (a.k.a. ''x86_64'' or ''amd64'') machines set up to run both Windows 7 and Debian Linux. When you came into the group, odds are a preconfigured workstation was placed in front of you, ready to rock. But how was it configured, you ask? Read on...

'''FIRST''', I recommend that you read this like a book, a manual of steps that you will follow in linear order. Failure to do so will make things difficult, if not impossible.

'''Second''', please understand that this process never goes the same way on any two workstations. I can't prepare you for every tiny little problem you may run into, but only set the most important, critical steps before you as a skeletal framework. Good luck, starfighter.

= Beginning =
It should be fairly obvious that you'll need an assembled PC to work with. Not so obvious is the software you'll need:

* Windows 7 x64
* Debian 7 x86_64

Other than operating system discs, you'll need the following Windows software discs:

* Microsoft Office 2010 32-bit
* CorelDRAW Graphics Suite X4
* EndNote X4 Media - Windows (These have machine-specific license keys!)

Finally, you'll need the administrator flash drive. You know the drive of which I speak. Keep it secret. Keep it safe.

= Windows =
This section details installing the Windows 7 OS and software.

== OS ==
Place the Windows 7 DVD into the drive and reboot the system. This will require the BIOS to be configured to boot optical discs before the hard drive. Once the prompt comes up, choose 'Install now'. Accept the license agreement and choose 'Custom' on the next screen.

You should now arrive at a screen that shows the [[:Wikipedia:Disk_partitioning|current partition state]] of the drive. First, click on 'Drive options (advanced)'. If partitions exist, delete them by selecting the partition in the list and then clicking 'Delete'. Now, click 'New' and enter a partition size (in MB) that equals about half the total drive space. It doesn't have to be exact; the partitioner will round to the nearest sector anyways. The installer will give you some garbage about creating extra special partitions for Windows system files, and that's fine. Once the Windows partition was made, proceed.

All the other options (time zone, language, etc.) will be self-explanatory. For automatic updates, choose 'Use recommended settings'. The installer will at some point ask for a user account and password; make this your cluster username and password, or the cluster username and password of whoever will use the system most.

== Updates ==
Once you've logged into your account, don't think that Windows is installed. It will need at least two hours of babysitting while it installs the largest pile of updates you've ever witnessed. You will repeat the following process until no more updates exist:

# Click on the Windows icon (for old-timers, that's the 'Start' button)
# Click on 'Control Panel'
# Click on 'System and Security'
# Click on 'Check for Updates' under the 'Windows Update' heading
# Click on 'Check for Updates' in the left-hand pane
# Install all available updates
# Restart the computer after updates install
# Go back to Step 1.

Patience, grasshopper.

== Configuration ==
You will have to configure a few things in Windows.

=== Power management ===
In ''Control Panel => System and Security => Power Options'', select '''High performance''' from the list. You may have to click 'Show additional plans' to see this option.

=== Remote desktop access ===
In ''Control Panel => System and Security => System'', select ''Remote settings'' in the left-hand pane. Under 'Remote Desktop', select ''Allow connections only from computers running Remote Desktop with Network Level Authentication (more secure)''.

== Software ==
Typical members of this group need a plentiful plethora of packages installed onto their Windows systems in order to function as researchers. Here's what you'll need to install:

* Google Chrome
* Anti-virus
* Adobe Reader
* Microsoft Office
* EndNote X4
* CorelDRAW X4
* ACD/NMR 12
* Java
* NMRViewJ
* PuTTY
* HP LaserJet drivers
* Dell Color Laser drivers

=== Chrome ===
Open Internet Explorer. Click the Stop button about a billion times until IE actually stops loading the page. Navigate to [http://www.google.com Google]. Take Google up on its recommendation to download Chrome. The rest is cake.

=== Anti-virus ===
Open Chrome and navigate to [http://is.unl.edu is.unl.edu]. Under 'Quick Picks', click on 'Anti-virus'. Click on 'DOWNLOAD HERE'. Click on 'WINDOWS 64bit Version'. The rest is cake.

=== Adobe Reader ===
Open Chrome and navigate to [http://get.adobe.com/reader get.adobe.com/reader]. The rest is cake.

=== Microsoft Office ===
Insert the Office DVD and select 'Run autorun.exe' when the popup comes up. The rest is cake.

=== EndNote X4 ===
Make sure any Microsoft Office programs are ''closed''. Insert the EndNote X4 CD and select 'Run autorun.exe' when the popup comes up. The rest is cake. Now, restart Windows and log back in. Then, open Microsoft Word. Click on 'EndNote X4' in the top bar. Then click on 'Go to EndNote'. If you get the message, ''Invalid Class String'', then go [http://help.thomson.com/default.asp?portalid=tsc&refid=TS_ENCWYWFAQ13 here] to find the solution.

=== CorelDRAW X4 ===
Insert the CorelDRAW DVD and follow the steps. The rest is cake.

=== ACD/NMR 12 ===
ACD Labs offers a free version of their 1D and 2D NMR processor software for academics. Open Chrome and navigate to [http://www.acdlabs.com/resources/freeware/nmr_proc/index.php this address], then click 'Download'. You'll need to set up a user account to download the software. Once you've got the installer downloaded, just run it and follow the steps. Yep, the rest is cake.

Alternatively, you should be able to run '''nmrproc_academia12.exe''' from '''Z:\bworley\admin\software''' without having to download anything or make any accounts.

=== Java ===
Open Chrome and navigate to [http://www.java.com/en/download/index.jsp this address]. Click on 'Free Java Download' and follow the steps. Cake.

=== NMRViewJ ===
This software is now non-free, but we have the last/latest available free version on the cluster. Run '''nvjinstall8_0_3.exe''' in '''Z:\bworley\admin\software\nmrviewj''' and follow the steps. Cake.

=== PuTTY ===
Best for last! Open Chrome and navigate to [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html this address]. Click on '''putty-0.62-installer.exe''' to download the installer. Run the installer; all the default options are fine.

Once PuTTY is installed, you'll need to insert the administrator flash drive. In the flash drive, go to '''ssh-rsa\clients\myusername''', where ''myusername'' is the cluster username that you're setting the computer up for. In that directory, there is an '''id_rsa.ppk''' file. Copy that file somewhere that only the current user has read access to, such as '''C:\Users\myusername'''. Now, open PuTTY and type ''myusername@bionmr-c1.unl.edu'' into both the 'Host Name' and 'Saved Sessions' text boxes. In the left-hand pane, click the plus sign next to 'SSH' and click on 'Auth'. Click 'Browse' and open the '''id_rsa.ppk''' file in the location you copied it to. Finally, click back to 'Session' in the left-hand pane and click 'Save' under 'Saved Sessions'.

You're ready to rock. Return the administrator flash drive to its sacred resting place.

=== Brother printer drivers ===
The Brother printer driver CDs are available in the lab office. Use those CDs to install drivers (only drivers, no software suites) for the two Brother printers outside the office. The IP addresses of the printers will be requested by the installer software; you can get those addresses by printing off the ''printer status'' information from each printer via their front panel buttons.

= Linux =
This section details installing and configuring the Linux OS.

== OS ==
Insert the Debian DVD and reboot the computer. When the Debian boot prompt comes up, press the Tab key, type '''desktop=xfce''', and hit enter. Most of the options will be self-explanatory until you get to the partitioning. You will select ''Use custom layout'' and click next.

The partitioning of linux systems in the group is done as follows:

* 128 MB of ext2 mounted on /boot (made at the beginning of the free space)
* All remaining space allocated as ext4 and mounted on '''/'''
* 2048 MB of swap (made at the end of the free space)

Make the partitions in the above order. After making the boot partition, subtract 2048 MB from the remaining free space to get the size of the '''/''' partition. Then use the rest of the free space (about 2048 MB, but it will rarely be exact) as swap.

You should now have a partitioning scheme that spans the entire disk that looks something like this:

* '''sda1:''' Windows system files (few hundred MB)
* '''sda2:''' Windows partition (few hundred GB, about half the drive)
* '''sda3:''' Linux boot partition (128 MB)
* '''sda4:''' Extended partition
* '''sda5:''' Linux root partition (few hundred GB, about half the drive)
* '''sda6:''' Linux swap partition (roughly 2048 MB)

Everything else will be much more self-explanatory, and the defaults are A-OK for almost all the other options.

== Configuration ==
You will have to configure the system a bit more to get it talking with the cluster and running properly. Once the system boots up, use '''Ctrl'''+'''Alt'''+'''F1''' to navigate to the terminal and log in as root. Once you're logged in, insert and mount the system administrator flash drive, like so:

mkdir /mnt/flash
mount /dev/sdb1 /mnt/flash

Where the above example assumes that ''/dev/sdb1'' is the flash drive device node. Once mounted, run the following commands:

cd /mnt/flash/admin-scripts/linux/workstations
./run

The script will ask if you're ready to proceed. As long as everything above went OK, it's safe to say 'yes' here. Hopefully, the script will complete without errors and your linux workstation will be properly configured. Unmount the flash drive:

cd
umount /mnt/flash
reboot

[[category:Sysadmin]]

Editing the group website

2013-07-25T17:53:26Z

Wiki Administrator:

The group website is located on [http://bionmr.unl.edu bionmr], in a typical [[:Wikipedia:LAMP_(software_bundle)|LAMP]] configuration. The server has no [[:Wikipedia:Network_File_System|NFS]] access, so the only way of editing pages is with '''vi''' via an '''ssh''' login. Also, as it has no [[:Wikipedia:File_Transfer_Protocol|FTP]] access, the only means of uploading files is '''scp''' or [[:Wikipedia:Server_Message_Block|Samba]]. Fear not! These methods are more secure, and are just as simple as those you already use. This page details how to edit the group website.

=ACHTUNG=
'''Please edit files on the website with ''extreme caution and respect''! Make sure you don't overwrite or delete files unless you're absolutely certain it's OK to do so.'''

=General website access=
You can log into the server and send files to the server with the '''ssh''' and '''scp''' commands, respectively. The following subsections detail how to do so.

==Logging into the server==
Logging into [http://bionmr.unl.edu bionmr] is done via simple keyed secure shell. You'll need the same RSA key, username and password. If you're on linux, you're already set up:

ssh bionmr.unl.edu

On windows, you'll need to copy the PuTTY session to a new name, and edit the hostname to ''bionmr''.

==Uploading files to the server==

===From Linux===
Pushing files to [http://bionmr.unl.edu bionmr] is done using the '''scp''' program, a remote file copy program similar to '''rcp''', but secured through [[:Wikipedia:Secure_Shell|SSH]]. To send a file to the server, use the following command (from a linux workstation):

scp /path/to/local/file bionmr.unl.edu:/tmp

Once you've logged into the server, the file(s) will be located in '''/tmp'''. You could also '''scp''' the files to your home directory on [http://bionmr.unl.edu bionmr], if you want to.

===From Windows===
To copy a file from a windows machine to [http://bionmr.unl.edu bionmr], map a network drive to '''\\bionmr\myusername''' where ''myusername'' is your user name. You can then copy files into that share, which is your home directory. From there, you can '''ssh''' into [http://bionmr.unl.edu bionmr] and play with the files as desired.

=Editing the website=

==Directory structure==
The website data is located in '''/var/www'''. Documents available on the top-level of the server are found here (e.g. [http://bionmr.unl.edu/nmr.php http://bionmr.unl.edu/nmr.php] will be '''nmr.php'''). Please notice that all the files are owned by the '''www-data''' user with rw-r--r-- (644) permissions. Directories are also owned by the '''www-data''' user with rwxr-xr-x (755) permissions.

Use the commands '''htdocs-cp''', '''htdocs-mv''', '''htdocs-mkdir''' and '''htdocs-vi''' instead of '''cp''', '''mv''', '''mkdir''' and '''vi'''.

A few special subdirectories exist here that you need to know about.

===courses===
The '''courses''' directory contains files for courses, rather unsurprisingly. Each subdirectory of '''courses''', such as '''courses/chem116''' has a file called '''content.php''' and directories organizing course content into groups like '''exams''', '''lectures''' and '''information'''. The directory names there are not set in stone; you just have to edit the '''content.php''' file to link to them, as detailed below.

===files===
The '''files''' directory contains non-image files that can be downloaded from the website. This directory contains a subdirectory for each top-level page, so if I make a link to a file called '''mydoc.pdf''' in '''proteins.php''', the file will reside in '''files/proteins/mydoc.pdf'''. More on this below.

===images===
The '''images''' directory contains image files. Images in each top-level page will be located in their own directory, named after the page, just like stuff in '''files'''. Sensing a theme, yet? ''':)'''

===include===
The '''include''' directory contains a library of [[:Wikipedia:PHP|PHP]] code that is used by pages in the top-level. Unless you're adding publication information to '''include/publication.php''', you probably won't need to edit anything here. Steer clear of here, ya hear?

==Template styling==
The pages in the website derive their style information from the [http://wdn.unl.edu UNL Templates], based on a [[:Wikipedia:PHP|PHP]] [[:Wikipedia:PEAR|PEAR]] framework provided by UNL. A good reference on the templates can be found [http://wdn.unl.edu/resources here]. However, while it's good to understand certain aspects of the UNL templates (e.g. content layouts), you ''will not be writing any [[:Wikipedia:HTML|HTML]]'', so don't bury yourself in the details there.

===Image size requirements===
Images on the website must conform to the current page style, so each type of image has size requirements, detailed below.

* Images inline with paragraphs of text must have width '''700px'''.
* Images in picture gallery sections: largest dimension (width or height) must not exceed '''750px'''.
* Images for group member pictures must be exactly '''210x158px'''.
* Images for new page links on ''nmr.php'' or ''software.php'' must be '''210x156px'''.

==PHP Function Reference==
If you need more information about the functions you're using in the top-level web pages, you can look (don't touch!) through the [[:Wikipedia:PHP|PHP]] files in the '''include''' directory. Each function will have a comment preceding it that describes - in graphic detail - the task it performs. Enjoy!

[[category:Sysadmin]]

Spec20

2013-05-11T06:10:56Z

Wiki Administrator:

==Purpose==

To find an unknown concentration of a solution by plotting known concentration of the same solution vs absorbance. A handout for the students is available here: [[File:Maxie_-_Spec20_Station_Handout.docx]].

==Experiment==

0. Preparation: Make sure the spectrometer wavelength is set to 590 nm. The instructions to calibrate the spectrometer is labeled on the front of each Spec20. Prepare six test tubes with percents ranging from 0% to 100% of blue dyes. Test tube 1 is water only it is to be used as the blank. Also every student should have one test tube labeled unknown.

1. Ask the students to draw two columns on a sheet of paper with PERCENT on top of column one and DATA on top of column two.

2. Ask the students to put test tube number 1(BLANK) into spec20. Check each station to make sure the absorbance reading is approximately is zero.

3. Ask the students to put test tube from number 2 to number 5 while reading off the reading corresponding percents 20%, 50%, 80% and 100% and tell them to record it in the PERCENT column as well as record the absorbance in the DATA column.

4. Ask the students to put the last test tube labeled "ev"(UNKNOWN) into the Spec20. Write down the absorbance reading in the data column and mark it as "x" in the percent column.

5. Inform the students to take the data sheets to the computer station.

[[Category:Maxey Demos]]

File:Maxie - Spec20 Station Handout.docx

2013-05-11T06:10:01Z

Wiki Administrator:

Computer station

2013-05-10T06:36:11Z

Wiki Administrator:

At the computer station, students will graph the data points they collected from the Spec20 station and draw three molecular structures. The handout to be given to students is available here: [[File:Maxey_-_Computer_Station_Handout.docx]].

== Preparation ==

''This should be ready the day before)''

* Six to eight volunteering laptops from group members should be provided and they are all set in a classroom in the Maxey elementary school.
* Set up an account for Maxey demo for each laptop.
* Install ChemBioDraw and KaleidaGraph software on each laptop.
* Set up wireless printer/router for each laptop.

== Experiment A - KaleidaGraph ==

KaleidaGraph is used for processing the Spec20 Data. ''(Make sure the students finish the Spec20 experiment before they come to this station.)''

# Click the first white box in the toolbar and you can open an empty spreadsheet with three columns.
# Input the data of concentration and absorbance in column A and B. (Do not input the percentage symbol or the unknown sample absorbance.)
# Go to “Gallery" from the menu, click “linear” then “scattering”, then there is a window popping up. Choose the A column to be the X-axis, B column to be the y-axis and click “new plot” icon down below.
# After you have the plot, change the title to be "Absorbance vs. concentration"
# Go to “file” and click “print graphics”.

== Experiment B - ChemDraw ==

Three molecules will be drawn by using ChemBioDraw: Acetic acid is the main component of vinegar. Acetylsalicylic acid is the active reagent of aspirin. Glucose is the major energy source in our body.

On the left side of the working window, a toolbar contains all the tools that are handy for drawing those molecules, such as single bonds, double bonds, benzene, texting and eraser.

# Find an empty place and draw the first bond by dragging the icon of a bond from the toolbar to that place and loose your mouse.
# Move the mouse to the end of that bond where you want to start another bond or a word (for example, "H" is for proton or hydrogen. "C" is for carbon and "O" is for oxygen).
# After drawing the molecule, use the “lasso” from the toolbar to select the whole molecule, and then go to the menu and select “convert structure to name”. Find out if you do the right thing by comparing the name that the computer tells you with the name you are supposed to draw.

[[Category:Maxey Demos]]

File:Maxey - Computer Station Handout.docx

2013-05-10T06:34:25Z

Wiki Administrator:

Computer station

2013-05-10T06:34:03Z

Wiki Administrator:

At the computer station, students will graph the data points they collected from the Spec20 station and draw three molecular structures. The handout to be given to students is attached to this wiki page.

== Preparation ==

''This should be ready the day before)''

* Six to eight volunteering laptops from group members should be provided and they are all set in a classroom in the Maxey elementary school.
* Set up an account for Maxey demo for each laptop.
* Install ChemBioDraw and KaleidaGraph software on each laptop.
* Set up wireless printer/router for each laptop.

== Experiment A - KaleidaGraph ==

KaleidaGraph is used for processing the Spec20 Data. ''(Make sure the students finish the Spec20 experiment before they come to this station.)''

# Click the first white box in the toolbar and you can open an empty spreadsheet with three columns.
# Input the data of concentration and absorbance in column A and B. (Do not input the percentage symbol or the unknown sample absorbance.)
# Go to “Gallery" from the menu, click “linear” then “scattering”, then there is a window popping up. Choose the A column to be the X-axis, B column to be the y-axis and click “new plot” icon down below.
# After you have the plot, change the title to be "Absorbance vs. concentration"
# Go to “file” and click “print graphics”.

== Experiment B - ChemDraw ==

Three molecules will be drawn by using ChemBioDraw: Acetic acid is the main component of vinegar. Acetylsalicylic acid is the active reagent of aspirin. Glucose is the major energy source in our body.

On the left side of the working window, a toolbar contains all the tools that are handy for drawing those molecules, such as single bonds, double bonds, benzene, texting and eraser.

# Find an empty place and draw the first bond by dragging the icon of a bond from the toolbar to that place and loose your mouse.
# Move the mouse to the end of that bond where you want to start another bond or a word (for example, "H" is for proton or hydrogen. "C" is for carbon and "O" is for oxygen).
# After drawing the molecule, use the “lasso” from the toolbar to select the whole molecule, and then go to the menu and select “convert structure to name”. Find out if you do the right thing by comparing the name that the computer tells you with the name you are supposed to draw.

[[Category:Maxey Demos]]

Computer station

2013-05-10T06:31:34Z

Wiki Administrator:

== Preparation ==

''This should be ready the day before)''

* Six to eight volunteering laptops from group members should be provided and they are all set in a classroom in the Maxey elementary school.
* Set up an account for Maxey demo for each laptop.
* Install ChemBioDraw and KaleidaGraph software on each laptop.
* Set up wireless printer/router for each laptop.

== Experiment A - KaleidaGraph ==

KaleidaGraph is used for processing the Spec20 Data. ''(Make sure the students finish the Spec20 experiment before they come to this station.)''

# Click the first white box in the toolbar and you can open an empty spreadsheet with three columns.
# Input the data of concentration and absorbance in column A and B. (Do not input the percentage symbol or the unknown sample absorbance.)
# Go to “Gallery" from the menu, click “linear” then “scattering”, then there is a window popping up. Choose the A column to be the X-axis, B column to be the y-axis and click “new plot” icon down below.
# After you have the plot, change the title to be "Absorbance vs. concentration"
# Go to “file” and click “print graphics”.

== Experiment B - ChemDraw ==

Three molecules will be drawn by using ChemBioDraw: Acetic acid is the main component of vinegar. Acetylsalicylic acid is the active reagent of aspirin. Glucose is the major energy source in our body.

On the left side of the working window, a toolbar contains all the tools that are handy for drawing those molecules, such as single bonds, double bonds, benzene, texting and eraser.

# Find an empty place and draw the first bond by dragging the icon of a bond from the toolbar to that place and loose your mouse.
# Move the mouse to the end of that bond where you want to start another bond or a word (for example, "H" is for proton or hydrogen. "C" is for carbon and "O" is for oxygen).
# After drawing the molecule, use the “lasso” from the toolbar to select the whole molecule, and then go to the menu and select “convert structure to name”. Find out if you do the right thing by comparing the name that the computer tells you with the name you are supposed to draw.

[[Category:Maxey Demos]]

PCA Utilities

2012-10-02T23:33:42Z

Wiki Administrator: /* Obtaining pca-utils */

The PCA Utilities package provides small software routines for plotting PCA/OPLS scores and building dendrograms based on those scores. This page outlines how to install and use the ''pca-utils'' software.

= Introductions =

== Obtaining ''pca-utils'' ==
You can obtain the source code to ''pca-utils'' by clicking [http://bionmr.unl.edu/pca-utils.php here].

== Installing ''pca-utils'' ==
The PCA utilities are a set of command line open-source UNIX/Linux programs. The software is highly portable: provided your distribution has glibc, it should compile without incident. Once you have the source code, run these commands to install it:

cd /path/to/source/tarball
tar xf pca-utils-YYYYMMDD.tar.gz
cd pca-utils-YYYYMMDD/
make
sudo make install

By default, the programs install to ''/usr/bin'', but you can easily change this by modifying the Makefile if you need to.

== Plotting scores with ellipses ==
[[File:Beatles-plot.png|thumb|right|300px|Example scores plot generated by '''pca-ellipses''']]
For an input list file called ''list.txt'', you can quickly generate a postscript plot file (in this case called ''plot.ps'') that shows your PCA scores with 95% confidence ellipses around each group:

pca-ellipses -1 44.4 -2 22.2 -i ''list.txt'' -k -o ''plot.ps''

In the above statement, the optional arguments ''-1'' and ''-2'' were used to set contributions of PC1 and PC2 to 44.4% and 22.2%, respectively. You can then edit ''plot.ps'' to your liking. If you need a bit more control over your output, you can generate '''gnuplot'''-readable ellipses instead like so:

pca-ellipses -i ''list.txt'' > ellipses.txt
awk -F '\t' '/^[0-9]/{print$3,$4}' ''list.txt'' > points.txt
gnuplot> plot 'points.txt' w p, 'ellipses.txt' w l

Of course, in the second case, you're free to style everything any way you like. Happy hacking!

== Plotting 3D scores with ellipsoids ==
That's right, ladies and gentlemen. You can plot 3D scores! Just use the ''pca-ellipsoids'' command:

pca-ellipsoids -1 44.4 -2 22.2 -3 11.1 -i ''list.txt'' > ''plotscript.plt''

This creates a '''gnuplot'''-syntax script file that you can open up in an interactive gnuplot session like so:

gnuplot
'''gnuplot>''' load 'plotscript.plt'

The above commands will open up a plot window containing the 3D plot, which you can manipulate with the mouse. Once you've found the optimal viewpoint to display the plot, copy the two ''view'' angles at the bottom left corner of the plot window. Then Add the following two lines to the top of the ''plotscript.plt'' file:

set terminal postscript enhanced color
set output 'plot.ps'

Also, change view angles to your values in the following line of the plot script:

set view 60, 35

In other words, change ''60'' and ''35'' to your view angles. Finally, create the postscript file by running '''gnuplot''' again:

gnuplot plotscript.plt

You'll then have a ''plot.ps'' file that can be opened in your favorite graphics editor of choice. Happy editing!

== Generating dendrograms ==
[[File:Beatles-tree.png|thumb|right|300px|Example postscript tree generated by '''pca-bootstrap''']]
Two complementary methods exist for generating trees. The first uses Euclidean distances and bootstrapping statistics, while the second uses Mahalanobis distances and p-values. For datasets containing well-separated groups in scores space, the bootstrapping method will do fine. However, highly separation in overlapped data may be better quantified with p-values in many cases.

=== Using bootstrapping ===
To build a simple tree that displays to the console for quick checks, just run something like this:

pca-bootstrap -i ''list.txt''

The default number of bootstrap iterations is 100, but ''pca-bootstrap'' can easily handle more. You can set the number of iterations to, say 1000, like so:

pca-bootstrap -i ''list.txt'' -n 1000

Everything looks good? You can save a postscript file using the ''-o'' flag:

pca-bootstrap -i ''list.txt'' -n 1000 -k -o ''tree.ps''

=== Using parameterizing ===
To build a simple tree that displays to the console for quick checks, just run something like this:

pca-dendrogram -i ''list.txt''

Everything looks good? You can save a postscript file using the ''-o'' flag:

pca-dendrogram -i ''list.txt'' -k -o ''tree.ps''

If everything works, the plots generated from these methods should look something like this:

+-----------------------------------------------------------George
|3.8e-11
| +-------------------------------------Ringo
+----------------------|1.3e-08
| +-----John
+-----------------------------|0.45
+------Paul

Use of ''pca-bootstrap'' will yield values at the nodes between 0 and 100, while ''pca-dendrogram'' will yield values between 0 and 1.

== Calculating p-values ==
If you just need p-values to accept the null hypothesis, you can use this command:

pca-overlap -i ''list.txt''

== Calculating basic statistics ==
If you're interested in basic information about each group, such as mean and/or covariance, you can use ''pca-stats'':

pca-stats -i ''list.txt''

Goodness, that was easy, wasn't it!?

== Generating random datasets ==
Mainly provided for entertainment value and development/debugging, ''pca-rand'' lets you generate list files that contain bivariate normally distributed point sets. Here's an example command (in the bash scripting language) to build a faux list file:

(pca-rand -H -L John -u '(-2,2)' -v '(2,0.6)' -r 45 -n 10;
pca-rand -L Paul -u '(-2,2)' -v '(2,0.6)' -r 135 -n 9;
pca-rand -L George -u '(3,-2)' -v '(4,3)' -r 120 -n 13;
pca-rand -L Ringo -u '(-1,-1)' -v '(2,2)' -r 0 -n 15) > ''list.txt''

No, you read that right. You can download the list file generated by a single run of this command here: [[File:Beatles.txt]].

= "Wait, I'm still confused" =
Remember that every command in the ''pca-utils'' package has a help message. Just run the command that you need information on with the ''--help'' flag to get a nice message on how to use that command. You can also find manual pages for each command, e.g.:

man pca-dendrogram

[[category:Protocols]]
[[category:Metabolomics]]

PCA Utilities

2012-08-21T03:07:42Z

Wiki Administrator: /* Obtaining pca-utils */

The PCA Utilities package provides small software routines for plotting PCA/OPLS scores and building dendrograms based on those scores. This page outlines how to install and use the ''pca-utils'' software.

= Introductions =

== Obtaining ''pca-utils'' ==
You can obtain the source code to ''pca-utils'' by clicking [http://bionmr.unl.edu/files/pca-utils/pca-utils-20120820.tar.gz here].

== Installing ''pca-utils'' ==
The PCA utilities are a set of command line open-source UNIX/Linux programs. The software is highly portable: provided your distribution has glibc, it should compile without incident. Once you have the source code, run these commands to install it:

cd /path/to/source/tarball
tar xf pca-utils-YYYYMMDD.tar.gz
cd pca-utils-YYYYMMDD/
make
sudo make install

By default, the programs install to ''/usr/bin'', but you can easily change this by modifying the Makefile if you need to.

== Plotting scores with ellipses ==
[[File:Beatles-plot.png|thumb|right|300px|Example scores plot generated by '''pca-ellipses''']]
For an input list file called ''list.txt'', you can quickly generate a postscript plot file (in this case called ''plot.ps'') that shows your PCA scores with 95% confidence ellipses around each group:

pca-ellipses -1 44.4 -2 22.2 -i ''list.txt'' -k -o ''plot.ps''

In the above statement, the optional arguments ''-1'' and ''-2'' were used to set contributions of PC1 and PC2 to 44.4% and 22.2%, respectively. You can then edit ''plot.ps'' to your liking. If you need a bit more control over your output, you can generate '''gnuplot'''-readable ellipses instead like so:

pca-ellipses -i ''list.txt'' > ellipses.txt
awk -F '\t' '/^[0-9]/{print$3,$4}' ''list.txt'' > points.txt
gnuplot> plot 'points.txt' w p, 'ellipses.txt' w l

Of course, in the second case, you're free to style everything any way you like. Happy hacking!

== Plotting 3D scores with ellipsoids ==
That's right, ladies and gentlemen. You can plot 3D scores! Just use the ''pca-ellipsoids'' command:

pca-ellipsoids -1 44.4 -2 22.2 -3 11.1 -i ''list.txt'' > ''plotscript.plt''

This creates a '''gnuplot'''-syntax script file that you can open up in an interactive gnuplot session like so:

gnuplot
'''gnuplot>''' load 'plotscript.plt'

The above commands will open up a plot window containing the 3D plot, which you can manipulate with the mouse. Once you've found the optimal viewpoint to display the plot, copy the two ''view'' angles at the bottom left corner of the plot window. Then Add the following two lines to the top of the ''plotscript.plt'' file:

set terminal postscript enhanced color
set output 'plot.ps'

Also, change view angles to your values in the following line of the plot script:

set view 60, 35

In other words, change ''60'' and ''35'' to your view angles. Finally, create the postscript file by running '''gnuplot''' again:

gnuplot plotscript.plt

You'll then have a ''plot.ps'' file that can be opened in your favorite graphics editor of choice. Happy editing!

== Generating dendrograms ==
[[File:Beatles-tree.png|thumb|right|300px|Example postscript tree generated by '''pca-bootstrap''']]
Two complementary methods exist for generating trees. The first uses Euclidean distances and bootstrapping statistics, while the second uses Mahalanobis distances and p-values. For datasets containing well-separated groups in scores space, the bootstrapping method will do fine. However, highly separation in overlapped data may be better quantified with p-values in many cases.

=== Using bootstrapping ===
To build a simple tree that displays to the console for quick checks, just run something like this:

pca-bootstrap -i ''list.txt''

The default number of bootstrap iterations is 100, but ''pca-bootstrap'' can easily handle more. You can set the number of iterations to, say 1000, like so:

pca-bootstrap -i ''list.txt'' -n 1000

Everything looks good? You can save a postscript file using the ''-o'' flag:

pca-bootstrap -i ''list.txt'' -n 1000 -k -o ''tree.ps''

=== Using parameterizing ===
To build a simple tree that displays to the console for quick checks, just run something like this:

pca-dendrogram -i ''list.txt''

Everything looks good? You can save a postscript file using the ''-o'' flag:

pca-dendrogram -i ''list.txt'' -k -o ''tree.ps''

If everything works, the plots generated from these methods should look something like this:

+-----------------------------------------------------------George
|3.8e-11
| +-------------------------------------Ringo
+----------------------|1.3e-08
| +-----John
+-----------------------------|0.45
+------Paul

Use of ''pca-bootstrap'' will yield values at the nodes between 0 and 100, while ''pca-dendrogram'' will yield values between 0 and 1.

== Calculating p-values ==
If you just need p-values to accept the null hypothesis, you can use this command:

pca-overlap -i ''list.txt''

== Calculating basic statistics ==
If you're interested in basic information about each group, such as mean and/or covariance, you can use ''pca-stats'':

pca-stats -i ''list.txt''

Goodness, that was easy, wasn't it!?

== Generating random datasets ==
Mainly provided for entertainment value and development/debugging, ''pca-rand'' lets you generate list files that contain bivariate normally distributed point sets. Here's an example command (in the bash scripting language) to build a faux list file:

(pca-rand -H -L John -u '(-2,2)' -v '(2,0.6)' -r 45 -n 10;
pca-rand -L Paul -u '(-2,2)' -v '(2,0.6)' -r 135 -n 9;
pca-rand -L George -u '(3,-2)' -v '(4,3)' -r 120 -n 13;
pca-rand -L Ringo -u '(-1,-1)' -v '(2,2)' -r 0 -n 15) > ''list.txt''

No, you read that right. You can download the list file generated by a single run of this command here: [[File:Beatles.txt]].

= "Wait, I'm still confused" =
Remember that every command in the ''pca-utils'' package has a help message. Just run the command that you need information on with the ''--help'' flag to get a nice message on how to use that command.

[[category:Protocols]]
[[category:Metabolomics]]

Main Page

2012-08-18T00:11:37Z

Wiki Administrator: /* Getting started */

'''Welcome to the BioNMR Wiki Page.'''

This wiki exists to provide better access to lab protocols for the Powers lab. It is not a replacement for lab notebooks. Feel free to begin documenting new lab protocols or procedures here, or even moving old protocols onto this wiki.

== Getting started ==
For those who need a quick and dirty introduction to MediaWiki formatting, try this reference card:
* [http://bionmr.unl.edu/w/MediaWikiRefCard.pdf MediaWiki Reference Card]

Other general MediaWiki information pages:
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]

=== Wiki Categories ===

[[Special:Categories|View All Categories]]

Commonly used Categories:

* [[:Category:Lab safety and management|Lab safety and management]]
* [[:Category:Protocols|Protocols]]
* [[:Category:Bioscreen|Bioscreen]]
* [[:Category:FAST-NMR|FAST-NMR]]
* [[:Category:SMACMS|SMACMS]]
* [[:Category:Molecular Docking|Molecular Docking]]
* [[:Category:Metabolomics|Metabolomics]]
* [[:Category:Maxey Demos|Maxey Demos]]

Editing the group website

2012-08-18T00:11:03Z

Wiki Administrator: /* Template styling */

The group website is located on [http://bionmr.unl.edu bionmr], in a typical [[:Wikipedia:LAMP_(software_bundle)|LAMP]] configuration. The server has no [[:Wikipedia:Network_File_System|NFS]] access, so the only way of editing pages is with '''vi''' via an '''ssh''' login. Also, as it has no [[:Wikipedia:File_Transfer_Protocol|FTP]] access, the only means of uploading files is '''scp''' or [[:Wikipedia:Server_Message_Block|Samba]]. Fear not! These methods are more secure, and are just as simple as those you already use. This page details how to edit the group website.

=ACHTUNG=
'''Please edit files on the website with ''extreme caution and respect''! Make sure you don't overwrite or delete files unless you're absolutely certain it's OK to do so.'''

=General website access=
You can log into the server and send files to the server with the '''ssh''' and '''scp''' commands, respectively. The following subsections detail how to do so.

==Logging into the server==
Logging into [http://bionmr.unl.edu bionmr] is identical to logging into [http://bionmr-c1.unl.edu bionmr-c1]. You'll need the same RSA key, username and password. If you're on linux, you're already set up:

ssh bionmr.unl.edu

On windows, you'll need to copy the PuTTY session to a new name, and edit the hostname to ''bionmr'' instead of ''bionmr-c1''.

==Uploading files to the server==

===From Linux===
Pushing files to [http://bionmr.unl.edu bionmr] is done using the '''scp''' program, a remote file copy program similar to '''rcp''', but secured through [[:Wikipedia:Secure_Shell|SSH]]. To send a file to the server, use the following command (from a linux workstation):

scp /path/to/local/file bionmr.unl.edu:/tmp

Once you've logged into the server, the file(s) will be located in '''/tmp'''. You could also '''scp''' the files to your home directory on [http://bionmr.unl.edu bionmr], if you want to.

===From Windows===
To copy a file from a windows machine to [http://bionmr.unl.edu bionmr], map a network drive to '''\\bionmr\myusername''' where ''myusername'' is your user name. You can then copy files into that share, which is your home directory. From there, you can '''ssh''' into [http://bionmr.unl.edu bionmr] and play with the files as desired.

=Editing the website=

==Directory structure==
The website data is located in '''/var/www/localhost/htdocs'''. Documents available on the top-level of the server are found here (e.g. [http://bionmr.unl.edu/nmr.php http://bionmr.unl.edu/nmr.php] will be '''nmr.php'''). Please notice that all the files are owned by the '''apache''' user with rw-r--r-- (644) permissions. To copy a file into this directory, use the following command:

sudo install -v -m 644 -o apache -g apache /path/to/file /var/www/localhost/htdocs/new-filename

Again, because files are owned by '''apache''', you have to use '''sudo vi''' to edit them. It's rare that you'll need to create a new directory, but in that case, you can use the following command:

sudo install -v -m 755 -o apache -g apache -d /var/www/localhost/htdocs/new-dirname

A few special subdirectories exist here that you need to know about.

===courses===
The '''courses''' directory contains files for courses, rather unsurprisingly. Each subdirectory of '''courses''', such as '''courses/chem116''' has a file called '''content.php''' and directories organizing course content into groups like '''exams''', '''lectures''' and '''information'''. The directory names there are not set in stone; you just have to edit the '''content.php''' file to link to them, as detailed below.

===files===
The '''files''' directory contains non-image files that can be downloaded from the website. This directory contains a subdirectory for each top-level page, so if I make a link to a file called '''mydoc.pdf''' in '''proteins.php''', the file will reside in '''files/proteins/mydoc.pdf'''. More on this below.

===images===
The '''images''' directory contains image files. Images in each top-level page will be located in their own directory, named after the page, just like stuff in '''files'''. Sensing a theme, yet? ''':)'''

===include===
The '''include''' directory contains a library of [[:Wikipedia:PHP|PHP]] code that is used by pages in the top-level. Unless you're adding publication information to '''include/publication.php''', you probably won't need to edit anything here. Steer clear of here, ya hear?

==Template styling==
The pages in the website derive their style information from the [http://wdn.unl.edu UNL Templates], based on a [[:Wikipedia:PHP|PHP]] [[:Wikipedia:PEAR|PEAR]] framework provided by UNL. A good reference on the templates can be found [http://wdn.unl.edu/resources here]. However, while it's good to understand certain aspects of the UNL templates (e.g. content layouts), you ''will not be writing any [[:Wikipedia:HTML|HTML]]'', so don't bury yourself in the details there.

===Image size requirements===
Images on the website must conform to the current page style, so each type of image has size requirements, detailed below.

* Images inline with paragraphs of text must have width '''700px'''.
* Images in picture gallery sections: largest dimension (width or height) must not exceed '''750px'''.
* Images for group member pictures must be exactly '''210x158px'''.
* Images for new page links on ''nmr.php'' or ''software.php'' must be '''210x156px'''.

==PHP Function Reference==
If you need more information about the functions you're using in the top-level web pages, you can look (don't touch!) through the [[:Wikipedia:PHP|PHP]] files in the '''include''' directory. Each function will have a comment preceding it that describes - in graphic detail - the task it performs. Enjoy!