Hi, You have two options to start out: traditional, or automated.
Traditional structure determination: 1. Run your shift table through TALOS (http://spin.niddk.nih.gov/bax/ software/TALOS/index.html) to get backbone torsion angle restraints. 2. Convert your assigned sparky NOE table to traditional xplor format. Offhand, I don't know of a script to do this. 3. Start with $xplor_dir/eginput/gb1_rdc/anneal.py. Change filenames as needed, and comment out RDC-specific lines if you don't have RDC data available. 4. Run with xplor -py anneal.py. 5. Analysis scripts are run automatically, so you can see best structures, their average, reports on violated restraints, etc. 6. Iterate, weeding out wrong NOESY assignments and adding in new assigned peaks. Automated structure determination: 1. Run your shift table through TALOS (http://spin.niddk.nih.gov/bax/ software/TALOS/index.html) to get backbone torsion angle restraints. 2. Start with $xplor_dir/eginput/marvin/cvn/initMatch*tcl. Change filenames as necessary. Should be able to read sparky shift table and peak location table directly. 3. Run TCL scripts in the directory as described in the README file. Running on a cluster is highly recommended. 4. Analysis scripts are run automatically. Will select converged structures, produce mean coordinates, and report accuracy & precision. 5. Convert high-likelihood peaks to traditional xplor format, for use in later refinement. If you have the computational resources (a cluster of 30 linux PCs can run a structure of a ~100 residue protein in a day or so), I'd suggest the automated route to start with. It begins with the shift table and unassigned NOESY peak location tables, so it's insensitive to any mistakes you might have made assigning your NOESY peaks. It's not guaranteed to converge, of course, but it's attractive for beginners, because it's quite tolerant of various types of errors, gets you an answer quickly, produces detailed assessments of the likelihood of the possible assignments of each NOESY peak, and is reproducible. So have a look at the scripts, decide how you want to proceed, and then we can answer your more specific questions. --JK On Feb 25, 2008, at 4:56 PM, nrpreddy at umich.edu wrote: > Dear Friends, > > I have just started using XPLOR-NIH. I have NOE restraints file saved > from Sparky after assiging NOESY spectrum. Can anyone please guide how > to proceed further for NMR structure calculations. I appreciate if > someone can guide me through this. > > Thanking you, > > -- > With Regards, > Ravi Prakash Reddy Nanga > > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
