Hello Simon-- > I am attempting to use a new python script to perform some PRE > calculations and I am using a structure containing 6 spin labels with > four orientations attached to a haem containing protein, and when I run > psfGen to obtain the psf file I get the following traceback: > > /afs/gorlaeus.net/lic/metprot/software/xplor-nih/2.22/python/psfGen.py:220: > DeprecationWarning: raising a string exception is deprecated > raise "residue %s not of type %s in %s" % (res,ret,`seq`) > Traceback (most recent call last): > File "<string>", line 1, in <module> > File > "/afs/gorlaeus.net/lic/metprot/software/xplor-nih/2.22/bin/pdb2psf", > line 47, in <module> > pdbToPSF(open(infile).read()) > File > "/afs/gorlaeus.net/lic/metprot/software/xplor-nih/2.22/python/psfGen.py", > line 588, in pdbToPSF > deprotonateHIS=False,customRename=customRename) > File > "/afs/gorlaeus.net/lic/metprot/software/xplor-nih/2.22/python/psfGen.py", > line 355, in seqToPSF > if seqType=='auto': seqType = deduceSeqType(seq) > File > "/afs/gorlaeus.net/lic/metprot/software/xplor-nih/2.22/python/psfGen.py", > line 220, in deduceSeqType > raise "residue %s not of type %s in %s" % (res,ret,`seq`) > Is there a way to do this in pyXplor or do I need to use the > old-fashioned xplor to achieve this?
You might check out eginput/pre/generate.py. Here's another example which uses a combination of scripts. This will be distributed in the next release of Xplor-NIH http://nmr.cit.nih.gov/pub/pre2.tar.gz hope it helps-- Charles -------------- next part -------------- Charles Schwieters email: Charles at Schwieters.org www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 198 bytes Desc: not available Url : http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20110914/885a0797/attachment-0001.bin
