University of Chicago:NMR Software Guide: Difference between revisions
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==Volume 2: A User’s Guide to NMRView with NvAssign== | ==Volume 2: A User’s Guide to NMRView with NvAssign== | ||
Overview<br> | |||
#Purpose<br> | |||
#General<br> | |||
#Helpful Concepts<br> | |||
#Platforms & Program versions<br> | |||
#Clicking<br> | |||
#Guide Nomenclature<br> | |||
Viewing and Plotting a 2D spectrum<br> | |||
#Presumptions<br> | |||
#Start NMRView<br> | |||
#Orient yourself<br> | |||
#Set Preferences (optional)<br> | |||
#Create a new window <br> | |||
#Bring your spectrum into the working memory<br> | |||
#Orient yourself with respect to the window menu and its options<br> | |||
#Draw your spectrum in the window you created<br> | |||
#Familiarize yourself with cursor functions and zooming in & out <br> | |||
#“Plotting” your spectrum<br> | |||
Picking and Assigning Peaks in a 2D spectrum<br> | |||
#Call up the peak picking window<br> | |||
#Adjust the appearance of your spectrum<br> | |||
#Select your peak picking parameters<br> | |||
#Pick the peaks<br> | |||
#Orient yourself with the Peak Panel<br> | |||
#Save your peak list as an .xpk file<br> | |||
#Couple multiple peaks that should be one peak<br> | |||
#Manually add and/or delete peaks to/from the peaklist<br> | |||
#Compress and Degap<br> | |||
#Manually assign residue identities to your peaks (optional)<br> | |||
Overlaying two 2D spectra<br> | |||
Measuring chemical shift differences between two 2D spectra<br> | |||
Obtaining distance restraints from a NOESY spectrum<br> | |||
Examining 3D spectra<br> | |||
NVAssign: Coordinating 3D Experiments to Achieve Total Assignment<br> | |||
#Overview<br> | |||
#Important details<br> | |||
#Preparation<br> | |||
##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 | |||
##D. Open NVAssign<br> | |||
#Read in your data<br> | |||
#Filter your peaks<br> | |||
#Cluster your peaks<br> | |||
#Edit your clusters<br> |
Revision as of 13:50, 19 December 2005
Volume 1: A User’s Guide to NMRPipe
1D Spectrum
- Overview
2D Spectrum
- 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”
- Convert the NMRPipe file “test.ft” to NMRView format
- You’re done!
Processing 3D Data
- 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!
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
Appendix 3: Troubleshooting
Volume 2: A User’s Guide to NMRView with NvAssign
Overview
- Purpose
- General
- Helpful Concepts
- Platforms & Program versions
- Clicking
- Guide Nomenclature
Viewing and Plotting a 2D spectrum
- 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 a 2D spectrum
- 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 two 2D spectra
Measuring chemical shift differences between two 2D spectra
Obtaining distance restraints from a NOESY spectrum
Examining 3D spectra
NVAssign: Coordinating 3D Experiments to Achieve Total Assignment
- 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
- D. Open NVAssign
- Read in your data
- Filter your peaks
- Cluster your peaks
- Edit your clusters