Charles,
Thanks I was able to get the script working but noticed the iupac labeling
isn't the same as that found in PDB files I have downloaded HB1 vs 1HB.
I should have clarified. I am trying to convert the structures into a form
that is depositable into the pdb.
This should be a very straight forward task considering the number of people
that use Xplor. I thought PDBTool was what I needed. It should allow me to
make remarks etc.
Here are my followup questions.
1. Is PDBTool what is typically used to convert xplor coordinate files into
depositable pdb files?
iupac naming convention?
2. If not, is there a script out there that does this? I saw the
xtal_submit.inp but that looked like it was for crystal structures.
3. SetsegName puts the text of a string in a location where in a pdb file
it corresponds to the atom type and the spacing isn't quite the same between
the second to last column and last column. I will need to modify the script
to put the atom type in this column for it to deposit correctly?
4. Do people add all the remarks found in most pdbs before submitting?
experimental conditions sequence etc?
regards,
Andrew
On 11/2/07, Charles at schwieters.org <Charles at schwieters.org> wrote:
>
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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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