Processing CEST Data - Revision history

Mjeppesen at 15:30, 9 September 2024

2024-09-09T15:30:56Z

← Older revision		Revision as of 15:30, 9 September 2024
Line 22:		Line 22:
	# Open test spectrum in nmrDraw		# Open test spectrum in nmrDraw
	# Pick peaks and save the peak list		# Pick peaks and save the peak list
	# Rename the peaks to their corresponding amino acid and residue #. Alternatively, create a peakList.txt with their IDs and run [https://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/~~caddA~~.py addA.py].		# Rename the peaks to their corresponding amino acid and residue #. Alternatively, create a peakList.txt with their IDs and run [https://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/addA.py addA.py].
	# Run [https://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/autoFit.tcl autoFit.tcl] in the c-shell.		# Run [https://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/autoFit.tcl autoFit.tcl] in the c-shell.
	##autoFit.tcl –specName fts/UBQ%03d.ft2 –inTab test.tab –series		##autoFit.tcl –specName fts/UBQ%03d.ft2 –inTab test.tab –series

Mjeppesen: Updated Links

2024-09-09T15:25:18Z

Updated Links

Mjeppesen at 00:04, 11 March 2022

2022-03-11T00:04:48Z

← Older revision		Revision as of 00:04, 11 March 2022
Line 30:		Line 30:
	# Then run ChemEx, check their tutorial		# Then run ChemEx, check their tutorial

	# Other Helpful Files: [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/calcFMFinput.py calcFMFinput.py] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/exp.cfg exp.cfg] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/fit.com fit.com] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/met.cfg met.cfg] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/par.cfg par.cfg]		Other Helpful Files: [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/calcFMFinput.py calcFMFinput.py] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/exp.cfg exp.cfg] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/fit.com fit.com] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/met.cfg met.cfg] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/par.cfg par.cfg]

	[[category:Needs_Updating]] <!--No idea what CEST Data is to link it correctly seems more like a protein file-->		[[category:Needs_Updating]] <!--No idea what CEST Data is to link it correctly seems more like a protein file-->
	[[category:Data_Processing_and_Analysis]]		[[category:Data_Processing_and_Analysis]]

Mjeppesen at 00:04, 11 March 2022

2022-03-11T00:04:34Z

← Older revision		Revision as of 00:04, 11 March 2022
Line 29:		Line 29:
	# Make sure the .out files are named like “A#N-HN.out”		# Make sure the .out files are named like “A#N-HN.out”
	# Then run ChemEx, check their tutorial		# Then run ChemEx, check their tutorial

			# Other Helpful Files: [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/calcFMFinput.py calcFMFinput.py] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/exp.cfg exp.cfg] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/fit.com fit.com] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/met.cfg met.cfg] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/par.cfg par.cfg]

	[[category:Needs_Updating]] <!--No idea what CEST Data is to link it correctly seems more like a protein file-->		[[category:Needs_Updating]] <!--No idea what CEST Data is to link it correctly seems more like a protein file-->
	[[category:Data_Processing_and_Analysis]]		[[category:Data_Processing_and_Analysis]]

Mjeppesen at 23:59, 10 March 2022

2022-03-10T23:59:21Z

← Older revision		Revision as of 23:59, 10 March 2022
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	##\| pipe2xyz –out fids/UBQ%03d.fid –y –ov		##\| pipe2xyz –out fids/UBQ%03d.fid –y –ov
	##/bin/rm –fr data/		##/bin/rm –fr data/
	# Run the fid.com script you just saved.		# Run the [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/fid.com fid.com] script you just saved.
	# Input file names and phase values into ftcpmg.com (follows this protocol) and run		# Input file names and phase values into [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/ftcpmg.com ftcpmg.com] (follows this protocol) and run
	# Open test spectrum in nmrDraw		# Open test spectrum in nmrDraw
	# Pick peaks and save the peak list		# Pick peaks and save the peak list
	# Rename the peaks to their corresponding amino acid and residue #. Alternatively, create a peakList.txt with their IDs and run ~~addASS~~.py.		# Rename the peaks to their corresponding amino acid and residue #. Alternatively, create a peakList.txt with their IDs and run [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/caddA.py addA.py].
	# Run autoFit.tcl in the c-shell.		# Run [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/autoFit.tcl autoFit.tcl] in the c-shell.
	##autoFit.tcl –specName fts/UBQ%03d.ft2 –inTab test.tab –series		##autoFit.tcl –specName fts/UBQ%03d.ft2 –inTab test.tab –series
	# Run extract_profiles_bru.py (follows)		# Run [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/extract_profiles_bru.py extract_profiles_bru.py] (follows)
	##./extract_profiles_bru.py –tbl nlin.tab –par fq3list –out fit/		##./extract_profiles_bru.py –tbl nlin.tab –par fq3list –out fit/
	# Make sure the .out files are named like “A#N-HN.out”		# Make sure the .out files are named like “A#N-HN.out”

Mjeppesen: quality of life updates

2022-01-20T06:16:32Z

quality of life updates

← Older revision		Revision as of 06:16, 20 January 2022
Line 2:		Line 2:


	# ~~Install~~ X11, nmrPipe, Python >=2.7, and ChemEx (from the Kay lab)		# Have X11, nmrPipe, Python >=2.7, and ChemEx (from the Kay lab) installed
	# Open a c-shell with “csh” and navigate to the directory with your ser file		# Open a c-shell with “csh” and navigate to the directory with your ser file
	# Open X11		# Open X11
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	# Then run ChemEx, check their tutorial		# Then run ChemEx, check their tutorial

	[[category:~~Protocols~~]]		[[category:Needs_Updating]] <!--No idea what CEST Data is to link it correctly seems more like a protein file-->
	[[category:Data_Processing_and_Analysis]]		[[category:Data_Processing_and_Analysis]]

Mjeppesen: LearningSorting

2021-09-11T04:44:20Z

LearningSorting

← Older revision		Revision as of 04:44, 11 September 2021
Line 30:		Line 30:
	# Then run ChemEx, check their tutorial		# Then run ChemEx, check their tutorial

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

Mjeppesen: Added to Category

2021-09-11T03:23:25Z

Added to Category

← Older revision		Revision as of 03:23, 11 September 2021
Line 29:		Line 29:
	# Make sure the .out files are named like “A#N-HN.out”		# Make sure the .out files are named like “A#N-HN.out”
	# Then run ChemEx, check their tutorial		# Then run ChemEx, check their tutorial

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

Jcatazaro at 21:38, 14 March 2017

2017-03-14T21:38:28Z

← Older revision		Revision as of 21:38, 14 March 2017
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	##y should be real with N total and valid points		##y should be real with N total and valid points
	##z should be the 15N dimension		##z should be the 15N dimension
	- zMODE Echo-Antiecho		## zMODE Echo-Antiecho
	- yMODE Real		## yMODE Real
	- aq2D States		## aq2D States
	# Save the script. It should look like the script that follows this protocol.		# Save the script. It should look like the script that follows this protocol.
	# Add these lines:		# Add these lines:

Jcatazaro: Created page with "Processing CEST Data # Install X11, nmrPipe, Python >=2.7, and ChemEx (from the Kay lab) # Open a c-shell with “csh” and navigate to the directory with your ser file # O..."

2017-03-14T21:37:59Z

Created page with "Processing CEST Data # Install X11, nmrPipe, Python >=2.7, and ChemEx (from the Kay lab) # Open a c-shell with “csh” and navigate to the directory with your ser file # O..."

New page

Processing CEST Data

# Install X11, nmrPipe, Python >=2.7, and ChemEx (from the Kay lab)
# Open a c-shell with “csh” and navigate to the directory with your ser file
# Open X11
# In the terminal type “bruker”
# Click “read parameters”
# Switch the F1 and F2 axes
##y should be real with N total and valid points
##z should be the 15N dimension
- zMODE Echo-Antiecho
- yMODE Real
- aq2D States
# Save the script. It should look like the script that follows this protocol.
# Add these lines:
##xyz2pipe –in fid/test%03d.fid –z –ri2c
##| pipe2xyz –out fids/UBQ%03d.fid –y –ov
##/bin/rm –fr data/
# Run the fid.com script you just saved.
# Input file names and phase values into ftcpmg.com (follows this protocol) and run
# Open test spectrum in nmrDraw
# Pick peaks and save the peak list
# Rename the peaks to their corresponding amino acid and residue #. Alternatively, create a peakList.txt with their IDs and run addASS.py.
# Run autoFit.tcl in the c-shell.
##autoFit.tcl –specName fts/UBQ%03d.ft2 –inTab test.tab –series
# Run extract_profiles_bru.py (follows)
##./extract_profiles_bru.py –tbl nlin.tab –par fq3list –out fit/
# Make sure the .out files are named like “A#N-HN.out”
# Then run ChemEx, check their tutorial

← Older revision		Revision as of 15:25, 9 September 2024
Line 18:		Line 18:
	##\| pipe2xyz –out fids/UBQ%03d.fid –y –ov		##\| pipe2xyz –out fids/UBQ%03d.fid –y –ov
	##/bin/rm –fr data/		##/bin/rm –fr data/
	# Run the [~~http~~://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/fid.com fid.com] script you just saved.		# Run the [https://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/fid.com fid.com] script you just saved.
	# Input file names and phase values into [~~http~~://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/ftcpmg.com ftcpmg.com] (follows this protocol) and run		# Input file names and phase values into [https://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/ftcpmg.com ftcpmg.com] (follows this protocol) and run
	# Open test spectrum in nmrDraw		# Open test spectrum in nmrDraw
	# Pick peaks and save the peak list		# Pick peaks and save the peak list
	# Rename the peaks to their corresponding amino acid and residue #. Alternatively, create a peakList.txt with their IDs and run [~~http~~://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/caddA.py addA.py].		# Rename the peaks to their corresponding amino acid and residue #. Alternatively, create a peakList.txt with their IDs and run [https://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/caddA.py addA.py].
	# Run [~~http~~://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/autoFit.tcl autoFit.tcl] in the c-shell.		# Run [https://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/autoFit.tcl autoFit.tcl] in the c-shell.
	##autoFit.tcl –specName fts/UBQ%03d.ft2 –inTab test.tab –series		##autoFit.tcl –specName fts/UBQ%03d.ft2 –inTab test.tab –series
	# Run [~~http~~://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/extract_profiles_bru.py extract_profiles_bru.py] (follows)		# Run [https://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/extract_profiles_bru.py extract_profiles_bru.py] (follows)
	##./extract_profiles_bru.py –tbl nlin.tab –par fq3list –out fit/		##./extract_profiles_bru.py –tbl nlin.tab –par fq3list –out fit/
	# Make sure the .out files are named like “A#N-HN.out”		# Make sure the .out files are named like “A#N-HN.out”
	# Then run ChemEx, check their tutorial		# Then run ChemEx, check their tutorial

	Other Helpful Files: [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/calcFMFinput.py calcFMFinput.py] [~~http~~://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/exp.cfg exp.cfg] [~~http~~://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/fit.com fit.com] [~~http~~://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/met.cfg met.cfg] [~~http~~://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/par.cfg par.cfg]		Other Helpful Files: [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/calcFMFinput.py calcFMFinput.py] [https://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/exp.cfg exp.cfg] [https://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/fit.com fit.com] [https://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/met.cfg met.cfg] [https://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/par.cfg par.cfg]

	[[category:Needs_Updating]] <!--No idea what CEST Data is to link it correctly seems more like a protein file-->		[[category:Needs_Updating]] <!--No idea what CEST Data is to link it correctly seems more like a protein file-->
	[[category:Data_Processing_and_Analysis]]		[[category:Data_Processing_and_Analysis]]