University of Chicago:NMR Software Guide: Difference between revisions
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=Processing NMR Data With OS X/Linux Freeware= | =Processing NMR Data With OS X/Linux Freeware= | ||
Based upon manuals by: | |||
'''Josh Kurutz, Ph.D.''' | |||
'''Technical Director''' | |||
'''Biochemistry & Molecular Biology NMR Facility''' | |||
'''University of Chicago''' | |||
<br>(Last offline revision: July 27, 2005)<br><br> | <br>(Last offline revision: July 27, 2005)<br><br> | ||
Line 22: | Line 16: | ||
==Volume 1: A User’s Guide to NMRPipe== | ==Volume 1: A User’s Guide to NMRPipe== | ||
===[[ | ===[[University_of_Chicago:NMR_Manual/V1S1 | 1D Data in NMRPipe]]<br>=== | ||
#Overview<br> | #Overview<br> | ||
===[[ | ===[[University_of_Chicago:NMR_Manual/V1S2 | 2D Data in NMRPipe]]<br>=== | ||
#Overview | #Overview | ||
#Start the program | #Start the program | ||
#Orient yourself | #Orient yourself | ||
#Convert Varian’s fid to an NMRPipe fid | #Convert Varian’s fid to an NMRPipe fid | ||
#Read in the NMRPipe-format 2D fid. | #Read in the NMRPipe-format 2D fid. | ||
#Process the first increment | #Process the first increment | ||
#Edit the script “process2d.com” | #Edit the script “process2d.com” | ||
#Execute the script “process2d.com” | #Execute the script “process2d.com” | ||
#Read the spectrum “test.ft” in the NMRPipe GUI | #Read the spectrum “test.ft” in the NMRPipe GUI | ||
#Phase the F1 dimension | #Phase the F1 dimension | ||
#Edit the script “process2d.com” again | #Edit the script “process2d.com” again | ||
#Re-run the script “process2d.com” | #Re-run the script “process2d.com” | ||
#Convert the NMRPipe file “test.ft” to NMRView format | #View the reprocessed 2D spectrum in the NMRPipe GUI | ||
#You’re done! | #Convert the NMRPipe file “test.ft” to NMRView format | ||
#You’re done! | |||
===[[ | ===[[University_of_Chicago:NMR_Manual/V1S3 | 3D Data in NMRPipe]]<br>=== | ||
#Convert the data<br> | #Convert the data<br> | ||
#Process & phase the first plane.<br> | #Process & phase the first plane.<br> | ||
Line 50: | Line 45: | ||
#You are done, done done!<br> | #You are done, done done!<br> | ||
<br> | <br> | ||
===[[Labs:University_of_Chicago:NMR_Manual:V2:S1 | Overview]]<br>=== | ==Volume 2: A User’s Guide to NMRView== | ||
===[[Labs:University_of_Chicago:NMR_Manual:V2:S1 | Overview of NMRView]]<br>=== | |||
#Purpose<br> | #Purpose<br> | ||
#General<br> | #General<br> | ||
Line 59: | Line 55: | ||
#Clicking<br> | #Clicking<br> | ||
#Guide Nomenclature<br> | #Guide Nomenclature<br> | ||
===[[Labs:University_of_Chicago:NMR_Manual:V2:S2 | | ===[[Labs:University_of_Chicago:NMR_Manual:V2:S2 | 2D Spectra in NMRView]]<br>=== | ||
#Presumptions<br> | #Presumptions<br> | ||
#Start NMRView<br> | #Start NMRView<br> | ||
Line 70: | Line 66: | ||
#Familiarize yourself with cursor functions and zooming in & out <br> | #Familiarize yourself with cursor functions and zooming in & out <br> | ||
#“Plotting” your spectrum<br> | #“Plotting” your spectrum<br> | ||
===[[Labs:University_of_Chicago:NMR_Manual:V2:S3 | Picking and Assigning Peaks in | ===[[Labs:University_of_Chicago:NMR_Manual:V2:S3 | Picking and Assigning Peaks in NMRView]]<br>=== | ||
#Call up the peak picking window<br> | #Call up the peak picking window<br> | ||
#Adjust the appearance of your spectrum<br> | #Adjust the appearance of your spectrum<br> | ||
Line 81: | Line 77: | ||
#Compress and Degap<br> | #Compress and Degap<br> | ||
#Manually assign residue identities to your peaks (optional)<br> | #Manually assign residue identities to your peaks (optional)<br> | ||
===[[Labs:University_of_Chicago:NMR_Manual:V2:S4 | Overlaying | ===[[Labs:University_of_Chicago:NMR_Manual:V2:S4 | Overlaying Spectra in NMRView]]<br>=== | ||
===[[Labs:University_of_Chicago:NMR_Manual:V2:S5 | Measuring | ===[[Labs:University_of_Chicago:NMR_Manual:V2:S5 | Measuring Chemical Shift Differences in NMRView]]<br>=== | ||
===[[Labs:University_of_Chicago:NMR_Manual:V2:S6 | Obtaining | ===[[Labs:University_of_Chicago:NMR_Manual:V2:S6 | Obtaining Distance Restraints in NMRView]]<br>=== | ||
===[[Labs:University_of_Chicago:NMR_Manual:V2:S7 | | ===[[Labs:University_of_Chicago:NMR_Manual:V2:S7 | 3D spectra in NMRView]]<br>=== | ||
===[[Labs:University_of_Chicago:NMR_Manual:V2:S8 | NVAssign | <br> | ||
==Volume 3: A User’s Guide to NVAssign== | |||
===[[Labs:University_of_Chicago:NMR_Manual:V2:S8 | NVAssign]]<br>=== | |||
#Overview<br> | #Overview<br> | ||
#Important details<br> | #Important details<br> | ||
Line 99: | Line 99: | ||
#Edit your clusters<br> | #Edit your clusters<br> | ||
<br> | <br> | ||
==Appendices== | ==Appendices== | ||
Latest revision as of 21:31, 2 January 2006
|
Processing NMR Data With OS X/Linux Freeware
Based upon manuals by:
Josh Kurutz, Ph.D.
Technical Director
Biochemistry & Molecular Biology NMR Facility
University of Chicago
(Last offline revision: July 27, 2005)
Volume 1: A User’s Guide to NMRPipe
1D Data in NMRPipe
- Overview
2D Data in NMRPipe
- Overview
- Start the program
- Orient yourself
- Convert Varian’s fid to an NMRPipe fid
- Read in the NMRPipe-format 2D fid.
- Process the first increment
- Edit the script “process2d.com”
- Execute the script “process2d.com”
- Read the spectrum “test.ft” in the NMRPipe GUI
- Phase the F1 dimension
- Edit the script “process2d.com” again
- Re-run the script “process2d.com”
- View the reprocessed 2D spectrum in the NMRPipe GUI
- Convert the NMRPipe file “test.ft” to NMRView format
- You’re done!
3D Data in NMRPipe
- Convert the data
- Process & phase the first plane.
- 3D processing with 2 scripts, LP in 15N only
- Processing 3D data using one script with LP in 13C and 15N
- Examine your 3D spectrum
- Convert the 3D nmrPipe spectrum to nmrView format.
- You are done, done done!
Volume 2: A User’s Guide to NMRView
Overview of NMRView
- Purpose
- General
- Helpful Concepts
- Platforms & Program versions
- Clicking
- Guide Nomenclature
2D Spectra in NMRView
- Presumptions
- Start NMRView
- Orient yourself
- Set Preferences (optional)
- Create a new window
- Bring your spectrum into the working memory
- Orient yourself with respect to the window menu and its options
- Draw your spectrum in the window you created
- Familiarize yourself with cursor functions and zooming in & out
- “Plotting” your spectrum
Picking and Assigning Peaks in NMRView
- Call up the peak picking window
- Adjust the appearance of your spectrum
- Select your peak picking parameters
- Pick the peaks
- Orient yourself with the Peak Panel
- Save your peak list as an .xpk file
- Couple multiple peaks that should be one peak
- Manually add and/or delete peaks to/from the peaklist
- Compress and Degap
- Manually assign residue identities to your peaks (optional)
Overlaying Spectra in NMRView
Measuring Chemical Shift Differences in NMRView
Obtaining Distance Restraints in NMRView
3D spectra in NMRView
Volume 3: A User’s Guide to NVAssign
NVAssign
- Overview
- Important details
- Preparation
- Process the necessary spectra and get them in NMRView format.
- Pick peaks in each of these spectra
- Change your default paths
- Review and edit your picked peaks in each spectrum
- Open NVAssign
- Read in your data
- Filter your peaks
- Cluster your peaks
- Edit your clusters
Appendices
Appendix 1: Phasing
- 1D phasing
- 1D Phasing theory
- Phasing indirectly-detected dimensions
- Relationship between phasing and first point multiplication
- Relationship between linear prediction and phasing
Appendix 2: Installing NMRPipe on a Mac
- Prepare your terminal windows to emulate “t c-shell”
- Edit your “tcshrc” file