Hello Yuan--
> > > > > I am trying to perform water refinement with the eginput/gb1_rdc/ > wrefine.py, and > > I needed to patch a cis-proline. I referred to a previously answered > post > back in > > 2013 (website link: http://article.gmane.org/ > > gmane.science.biology.xplor-nih.general/1718/match= > cis+proline+water+refinement), > > and added the following lines as indicated in the post: > > > > import psfGen > > protocol.loadPDB(inputStructures[1],deleteUnknownAtoms=True) > > xplor.command('''patch CIPP reference=nil=(resid 202)''') > > > > Instead of this line, please try: > psfGen.cisPeptide(202) > > If this doesn't work, I'll make certain to fix it. > > > Thank you for your reply! I actually started with psfGen.cisPeptide(202) > command, > and it did not find a C atom in the patch. Before this, I actually > successfully > used psfGen.cisPeptide(202) command for regulHere is the log indicating the > error > message: > > wrefine.py(32): psfGen.cisPeptide(201) > X-PLOR> > X-PLOR> patch CIPP > PATCH> reference=-=( resid 201 and segid "A") > SELRPN: 19 atoms have been selected out of 2288 > PATCH> reference=+=( resid 202 and segid "A") > SELRPN: 14 atoms have been selected out of 2288 > PATCH> end > %PATCH-ERR: atom C not found > > My guess is the CIPP patch in water refinement topology needs to be modified? You are correct- the cisPeptide function in Xplor-NIH 2.38 does not correctly deal with the topology used for water refinement. I've placed an updated, fixed version of psfGen.py here: http://nmr.cit.nih.gov/xplor-nih/updates/current/ By the way, the patch command you sent in your original message was simply missing and end statement. Also, please not that the residue number specified to cisPeptide is the residue before the peptide bond to be changed. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
