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Hello Andrew--
> Everyone has been a great help with the questions I had about final
> structures, thank you. Now I need to convert the xplor format to pdb
> format. I need to change the atom names, add a chainID etc.
The atom renaming *should* work fine. Please see below. Unfortunately,
the released version of Xplor-NIH will not write into the chainID
field. You could wait until December for the next release, or request a
prerelease version from me.
Please see below for the name conversion.
best regards--
Charles
>
> xplor.parseArguments()
> psffile="sh3.psf"
>
> import protocol
> protocol.initParams("protein")
> protocol.initStruct(psffile)
> from pdbTool import PDBTool
> PDBTool("ave.pdb").read()
for atom in AtomSel("known"):
atom.setSegmentName("A")
outfile=PDBTool("out.pdb")
outfile.useIupacNames()
outfile.addRemark("a string")
# this works in the next version of Xplor-NIH:
# outfile.setWriteChainID(1)
outfile.write()
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