University of Chicago:NMR Software Guide

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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

1. Overview
   

2D Data in NMRPipe

1. Overview
2. Start the program
3. Orient yourself
4. Convert Varian’s fid to an NMRPipe fid
5. Read in the NMRPipe-format 2D fid.
6. Process the first increment
7. Edit the script “process2d.com”
8. Execute the script “process2d.com”
9. Read the spectrum “test.ft” in the NMRPipe GUI
10. Phase the F1 dimension
11. Edit the script “process2d.com” again
12. Re-run the script “process2d.com”
13. View the reprocessed 2D spectrum in the NMRPipe GUI
14. Convert the NMRPipe file “test.ft” to NMRView format
15. You’re done!

3D Data in NMRPipe

1. Convert the data
   
2. Process & phase the first plane.
   
3. 3D processing with 2 scripts, LP in 15N only
   
4. Processing 3D data using one script with LP in 13C and 15N
   
5. Examine your 3D spectrum
   
6. Convert the 3D nmrPipe spectrum to nmrView format.
   
7. You are done, done done!
   

Volume 2: A User’s Guide to NMRView

Overview of NMRView

1. Purpose
   
2. General
   
3. Helpful Concepts
   
4. Platforms & Program versions
   
5. Clicking
   
6. Guide Nomenclature
   

2D Spectra in NMRView

1. Presumptions
   
2. Start NMRView
   
3. Orient yourself
   
4. Set Preferences (optional)
   
5. Create a new window
   
6. Bring your spectrum into the working memory
   
7. Orient yourself with respect to the window menu and its options
   
8. Draw your spectrum in the window you created
   
9. Familiarize yourself with cursor functions and zooming in & out
   
10. “Plotting” your spectrum
    

Picking and Assigning Peaks in NMRView

1. Call up the peak picking window
   
2. Adjust the appearance of your spectrum
   
3. Select your peak picking parameters
   
4. Pick the peaks
   
5. Orient yourself with the Peak Panel
   
6. Save your peak list as an .xpk file
   
7. Couple multiple peaks that should be one peak
   
8. Manually add and/or delete peaks to/from the peaklist
   
9. Compress and Degap
   
10. Manually assign residue identities to your peaks (optional)
    

Volume 3: A User’s Guide to NVAssign

NVAssign

1. Overview
   
2. Important details
   
3. 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
     
4. Read in your data
   
5. Filter your peaks
   
6. Cluster your peaks
   
7. Edit your clusters
   

Appendices

Appendix 1: Phasing

1. 1D phasing
   
2. 1D Phasing theory
   
3. Phasing indirectly-detected dimensions
   
4. Relationship between phasing and first point multiplication
   
5. Relationship between linear prediction and phasing
   

Appendix 2: Installing NMRPipe on a Mac

1. Prepare your terminal windows to emulate “t c-shell”
   
2. Edit your “tcshrc” file