University of Chicago:NMR Software Guide: Difference between revisions
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===[[University_of_Chicago:NMR_Manual/V1S2 | 2D Data in NMRPipe]]<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>=== | ===[[University_of_Chicago:NMR_Manual/V1S3 | 3D Data in NMRPipe]]<br>=== |
Revision as of 17:15, 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