Hi All,
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?
Alternatively, is there a way to re-number residues in a psf to
correspond with those in a pdb file?
Regards
Simon
--
Simon P Skinner
Protein Chemistry Group
Leiden Institute of Chemistry, Universiteit Leiden
Phone: +31 71 527 6089 / Fax: +31 71 527 4349
E-mail : skinnersp at chem.leidenuniv.nl
