2D NMR Analysis (CCPNMR) - Revision history

Mjeppesen at 05:20, 20 January 2022

2022-01-20T05:20:35Z

← Older revision		Revision as of 05:20, 20 January 2022
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	If you have problems opening the spectrum and you get an error message that reads: dimtype not....etc., go upstairs and process/phase the data upstairs in topspin instead of using NMRpipe. Then transfer the files using Gambrinus. For some reason sometimes it won't open unless you do it that way.		If you have problems opening the spectrum and you get an error message that reads: dimtype not....etc., go upstairs and process/phase the data upstairs in topspin instead of using NMRpipe. Then transfer the files using Gambrinus. For some reason sometimes it won't open unless you do it that way.

	[[category:~~Protocols~~\|NMR Analysis (CCPNMR) 2D]]		[[category:Needs_Updating\|NMR Analysis (CCPNMR) 2D]]
	[[category:Data_Processing_and_Analysis\|NMR Analysis (CCPNMR) 2D]]		[[category:Data_Processing_and_Analysis\|NMR Analysis (CCPNMR) 2D]]

Mjeppesen: LearningSorting

2021-09-11T04:25:34Z

LearningSorting

← Older revision		Revision as of 04:25, 11 September 2021
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	If you have problems opening the spectrum and you get an error message that reads: dimtype not....etc., go upstairs and process/phase the data upstairs in topspin instead of using NMRpipe. Then transfer the files using Gambrinus. For some reason sometimes it won't open unless you do it that way.		If you have problems opening the spectrum and you get an error message that reads: dimtype not....etc., go upstairs and process/phase the data upstairs in topspin instead of using NMRpipe. Then transfer the files using Gambrinus. For some reason sometimes it won't open unless you do it that way.

	[[category:Protocols\|~~Protocols~~]]		[[category:Protocols\|NMR Analysis (CCPNMR) 2D]]
	[[category:Data_Processing_and_Analysis]]		[[category:Data_Processing_and_Analysis\|NMR Analysis (CCPNMR) 2D]]

Mjeppesen: Added to Category

2021-09-11T03:22:33Z

Added to Category

← Older revision		Revision as of 03:22, 11 September 2021
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	If you have problems opening the spectrum and you get an error message that reads: dimtype not....etc., go upstairs and process/phase the data upstairs in topspin instead of using NMRpipe. Then transfer the files using Gambrinus. For some reason sometimes it won't open unless you do it that way.		If you have problems opening the spectrum and you get an error message that reads: dimtype not....etc., go upstairs and process/phase the data upstairs in topspin instead of using NMRpipe. Then transfer the files using Gambrinus. For some reason sometimes it won't open unless you do it that way.

			[[category:Protocols\|Protocols]]
			[[category:Data_Processing_and_Analysis]]

Jcatazaro at 15:31, 20 March 2017

2017-03-20T15:31:16Z

← Older revision		Revision as of 15:31, 20 March 2017
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	==Problems Opening==		==Problems Opening==

	If you have problems opening the spectrum and you get an error message that reads: dimtype not....etc., go upstairs and process/phase the data upstairs in topspin instead of using NMRpipe. Then transfer the files using Gambrinus. For some reason sometimes it won't open unless you do it that way.		If you have problems opening the spectrum and you get an error message that reads: dimtype not....etc., go upstairs and process/phase the data upstairs in topspin instead of using NMRpipe. Then transfer the files using Gambrinus. For some reason sometimes it won't open unless you do it that way.

	~~[[Category:Protocols]]~~
	~~[[Category:Metabolomics]]~~

Dmarshall at 22:26, 11 August 2015

2015-08-11T22:26:56Z

← Older revision		Revision as of 22:26, 11 August 2015
Line 58:		Line 58:

	Now you can drag and drop the file into CorelDraw or other software		Now you can drag and drop the file into CorelDraw or other software

			==Problems Opening==

			If you have problems opening the spectrum and you get an error message that reads: dimtype not....etc., go upstairs and process/phase the data upstairs in topspin instead of using NMRpipe. Then transfer the files using Gambrinus. For some reason sometimes it won't open unless you do it that way.

	[[Category:Protocols]]		[[Category:Protocols]]
	[[Category:Metabolomics]]		[[Category:Metabolomics]]

Dmarshall: /* Opening Spectra */

2015-08-11T20:51:35Z

Opening Spectra

← Older revision		Revision as of 20:51, 11 August 2015
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	Repeat these steps for any other spectra that you want opened and you can overlay the spectra		Repeat these steps for any other spectra that you want opened and you can overlay the spectra

	*To toggle between spectra, click on the “spectra” button on the spectra window and then toggle between the spectra that you want shown		* To toggle between spectra, click on the “spectra” button on the spectra window and then toggle between the spectra that you want shown

	*To change the color of the spectra and to toggle the dotted boxed line on and off, go to the “experiment” tab and choose “spectra” and go to the second tab in the pop-up window		* To change the color of the spectra and to toggle the dotted boxed line on and off, go to the “experiment” tab and choose “spectra” and go to the second tab in the pop-up window

	==Peak Picking==		==Peak Picking==

Dmarshall at 20:51, 11 August 2015

2015-08-11T20:51:03Z

← Older revision		Revision as of 20:51, 11 August 2015
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	~~'''~~Opening Spectra~~'''~~		==Opening Spectra==

	Go to the “Project” tab and “open spectra”		Go to the “Project” tab and “open spectra”
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	*To change the color of the spectra and to toggle the dotted boxed line on and off, go to the “experiment” tab and choose “spectra” and go to the second tab in the pop-up window		*To change the color of the spectra and to toggle the dotted boxed line on and off, go to the “experiment” tab and choose “spectra” and go to the second tab in the pop-up window

	~~'''~~Peak Picking~~'''~~		==Peak Picking==

	Hold control and shift down while clicking and dragging over area that you want peak picked		Hold control and shift down while clicking and dragging over area that you want peak picked
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	Click on the “Peak” tab and click “peak lists”. The peak table tab will show you the peaks that you selected on a table		Click on the “Peak” tab and click “peak lists”. The peak table tab will show you the peaks that you selected on a table

	~~'''~~Assigning Peak Resonance~~'''~~		==Assigning Peak Resonance==

	Go to peak table and click on Assign F1. Choose “new”, then “select option”. Then “set resonance name” and name it.		Go to peak table and click on Assign F1. Choose “new”, then “select option”. Then “set resonance name” and name it.
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	Repeat for all spin systems		Repeat for all spin systems

	~~'''~~Exporting Spectra~~'''~~		==Exporting Spectra==

	Go to the window tab		Go to the window tab

Dmarshall at 20:49, 11 August 2015

2015-08-11T20:49:53Z

← Older revision		Revision as of 20:49, 11 August 2015
Line 58:		Line 58:

	Now you can drag and drop the file into CorelDraw or other software		Now you can drag and drop the file into CorelDraw or other software

			[[Category:Protocols]]
			[[Category:Metabolomics]]

Dmarshall: Created page with "'''Opening Spectra''' Go to the “Project” tab and “open spectra” Change the file format to “Bruker” Change file type to “All” Find the spectrum you want..."

2015-08-11T20:48:48Z

Created page with "'''Opening Spectra''' Go to the “Project” tab and “open spectra” Change the file format to “Bruker” Change file type to “All” Find the spectrum you want..."

New page

'''Opening Spectra'''

Go to the “Project” tab and “open spectra”

Change the file format to “Bruker”

Change file type to “All”

Find the spectrum you want to open in your documents folder and choose the “proc” file

Rename the file (ex: HSQC_10)

Click on “Open Spectrum”

Reference the ppm (change the numbers)

Click on “commit” and choose “close-all done”

Repeat these steps for any other spectra that you want opened and you can overlay the spectra

*To toggle between spectra, click on the “spectra” button on the spectra window and then toggle between the spectra that you want shown

*To change the color of the spectra and to toggle the dotted boxed line on and off, go to the “experiment” tab and choose “spectra” and go to the second tab in the pop-up window

'''Peak Picking'''

Hold control and shift down while clicking and dragging over area that you want peak picked

Then you can delete peaks by clicking on peak (hold shift for multiple) and right-clicking on the peak. Then click on “peak” and “delete selected”.

Click on the “Peak” tab and click “peak lists”. The peak table tab will show you the peaks that you selected on a table

'''Assigning Peak Resonance'''

Go to peak table and click on Assign F1. Choose “new”, then “select option”. Then “set resonance name” and name it.

Repeat for F2

If they’re the same spin system, then click “set same spin system”

Repeat “assign resonance name” for all other peaks that belong to same spin system but don’t click “set same spin system” again.

Once done, go to “resonance” tab and click on “Resonances”. Highlight all that are in same spin system and click “add to spin system”.

Click the spin system that they belong to and the software will label them as the same spin system.

Repeat for all spin systems

'''Exporting Spectra'''

Go to the window tab

Click on “print window”

Set your parameters

Click on “save print file”

Now you can drag and drop the file into CorelDraw or other software