[Biopython-dev] changing PDB file chains

[David Cain]

Yes, John, it's possible!

You'll first want to modify the parsed structure. Add your water molecules
to the desired chain (removing from the old, of course). To actually do
this, you may want to look at the source (
http://biopython.org/DIST/docs/api/Bio.PDB-module.html), specifically how
the SMRCA hierarchy is constructed.

Once you've modified your Structure (say it's in a variable `struct`), you
should create an instance of PDBIO(), then save your structure like so:

pdb_writer = PDB.PDBIO()
pdb_writer.set_structure(struct)
pdb_writer.save("output_path.pdb")

Do not that PDBIO has some limitations (e.g. it cannot write out PDB header
data). It should probably suffice for your needs, though.

If you're not able to figure it out, feel free to email me back (preferably
with your code!) and I can help you out.
StackOverflow<http://stackoverflow.com> works
particularly well for me, if you're amenable to that.



David Cain
+1 (339) 222 4452


On Thu, Jun 13, 2013 at 3:01 PM, John Berrisford <jmb at ebi.ac.uk> wrote:

> Hi
>
>
>
> I'm trying to use biopython to update a PDB file.
>
>
>
> I'm trying to update the chain ID of a series of waters in a PDB file. I
> have the original chain ID, new chain ID and water residue number in an
> mmcif file which I parse using a separate parser. Then for each water I
> have
> in the mmcif file I want to update the chain ID from the cif file.
>
> I then want to write out the updated water line (to test it works) or write
> out the updated PDB file.
>
>
>
> Is this possible with biopython?
>
>
>
> Regards
>
>
>
> John
>
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