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Dear friends,

I had a mutation in my protein and now I have some amino acids around mutation remained unassigned. To get a way to find the missing peaks I modelled the mutated protein with modeller and out of the pdb file I got the chemical shift predictions using SPARTA. Now that I have chemical shift predictions I want to plot them like a spectra and overlay them to my real spectra to see if it will help me to assign some of the missing peaks. I know for solid-state NMR there is a software, but what about solution NMR?

Looking forward to hearing from you.

Thanks! Mahnaz

asked Nov 18 '10 at 05:50

Dummy's gravatar image


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NMRPipe has a script "cs2pk.tcl" which can be used to help create qualitative versions of various types of spectra starting from an NMRPipe-format chemical shift table.

The script will make a peak table from the input shifts, and generate scripts to build a simulated FID from the peak table. The intensities and linewidths will be uniform.

For example, this will make a crude 2D 1N15-HSQC fid (type HN) from input shift table "csPred.tab" ... it will create an output peak table "hn.tab" and a script "hn.com" which will simulate the FID:

cs2pk.tcl -in csPred.tab -out hn.tab -com hn.com -sim hn.fid -type HN -ref None -noise 10

You can do the same for other common experiments like HNCA etc. You can also supply a reference conversion command (as created by "bruker" or "varian") so that the simulation parameters used to generate the simulated FID can be set to match a given set of experimental data.

cheerful regards,

big fd


answered Nov 18 '10 at 11:30

delaglio's gravatar image


Thanks a milion Dr. Delaglio! I didn't know the solution is in nmrPipe! I will do it as soon as I solve the problem of adding chain B chemical shift data to chain A. - Dummy (Nov 19 '10 at 01:54)

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