Hi Charles Thanks for the quick fix - that's done the job.
cheers Richard ________________________________________ From: Charles Schwieters [[email protected]] Sent: Monday, April 01, 2013 11:37 AM To: Richard Harris Cc: xplor-nih at nmr.cit.nih.gov Subject: Re: [Xplor-nih] adding cis Proline in water refinment Hello Richard-- > > I'm trying to include a cisProline in water refinement calculations - > I'm > using a modified version of the script found in > eginput/gb1_rdc/wrefine.py. > In earlier posts on this matter its suggested that there are two ways > of > doing this: > > 1) load a pre-generated PSF using protocol.initStruct, and then load > the structure with protocol.initCoords instead of > protocol.loadPDB. This will not work unless, in generating your psf, you use the water refinement topology files as specified in wrefine.py. A psf generated using standard Xplor-NIH topology settings will not work with water refinement. > > 2) load the structure with protocol.loadPDB, and then correct the PSF > information using psfGen.cisPeptide. > > In the script I have: > import psfGen > protocol.loadPDB(inputStructures[0],deleteUnknownAtoms=True) > psfGen.cisPeptide(110) Unfortunately, the definition of the ``patch'' differs between standard Xplor-NIH topologies and those used for water refinement. The only way to do this on the fly here is to call the old XPLOR command xplor.command(''' patch CIPP reference=nil=(resid XX) ''') replacing XX with the appropriate residue number. psfGen.cisPeptide should be fixed to give a more appropriate error message. best regards-- Charles
