Hi Engin, thank you for your reply. That is exactly what I wanted. I just forgot the correct syntax. Actually, I could not find these words in the documentaion. I guess, they are very well hidden. Maia Engin Ozkan wrote:Am I missing something? How about this refinement.ncs.restraint_group { reference = chain A and not (resid 125 or resid 248 or ...) selection = chain B and not (resid 125 or resid 248 or ...) } as it is in http://www.phenix-online.org/documentation/ I don't think this is harder than excluding residues with an "option". Engin On 6/27/09 10:28 AM, Pavel Afonine wrote:Hi Maia,I made all restraint_groups in my parameter file. It's just too many of them. I thought that may be there is an option to say exclude residues 125, 248 etc.No - there is no such command: you need to edit selections manually.By the way, I have excessive_distance_limit = None. If I change it to some number, how does it work? the violating residues will be excluded or the whole molecule will?I'm not sure, Ralf knows this better. Ralf, could you comment on this please? My guess, that all this parameter does is it checks the distances between atoms in NCS copies and if there is a distance larger than excessive_distance_limit, then phenix.refine stops and tells you this. Pavel. _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111