1
|
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 |
|
2
|
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 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) |
