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)

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!

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)

NVAssign

 * 1) Overview
 * 2) Important details
 * 3) Preparation
 * 4) *Process the necessary spectra and get them in NMRView format.
 * 5) *Pick peaks in each of these spectra
 * 6) *Change your default paths
 * 7) *Review and edit your picked peaks in each spectrum
 * 8) *Open NVAssign
 * 9) Read in your data
 * 10) Filter your peaks
 * 11) Cluster your peaks
 * 12) Edit your clusters

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