University of Chicago:NMR Software Guide

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

Processing a 1D Spectrum

1. Overview
   

Processing a 2D Spectrum

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. Convert the NMRPipe file “test.ft” to NMRView format
    
14. You’re done!
    

Processing 3D Data

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!
   

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
   

Volume 2: A User’s Guide to NMRView with NvAssign

Overview

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

Viewing and Plotting a 2D spectrum

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 a 2D spectrum

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)
    

NVAssign: Coordinating 3D Experiments to Achieve Total Assignment

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