Hello Mark-- > > I am solving some NMR structures of cyclic peptides in CYANA. I am > trying to use XPLOR-NIH to add water-refinement. I have XPLOR-NIH vs > 2.39 and have been trying to use the script in > > xplor-nih/2.39/eginput/gb1_rdc/wrefine.py
I strongly suggest that you first upgrade to Xplor-NIH version 3.4 > > At the moment I think I need to do the following: > > -> final.pdb -- [final CYANA structure containing 20 models] --> > -convert all CYSS residues to CYS; rename 'NH2' (C-terminal > -amidation) from ATOM to HETATM > --> convert dihedral angle restraints to XPLOR-NIH format. > --> convert final CYANA noesy peak list files (currently in .peaks > -format) to XPLOR format. > > Could you advise on how best to convert the dihedral angle > restraints and noesy peak lists to the xplor format. One option would be to first convert your CYANA restraints to NEF format, and then use those in Xplor-NIH. This will require bits of the script eginput/gb1_rdc/refine_nef.py. I am certain that there are other ways to convert restraints, but I am no expert. > Also, can the > water refine script handle all 20 structures in the same pdb final, > or do I need to separate these? > It is easiest to split the structures into separate files. best regards-- Charles ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
