[Biopython] writing a PDB----PLEASEEEE HELP

[Lapointe, David]

Hi Martin,

If you  look at the PDB structure files based on NMR determinations, you'll see that they contain different models. Perhaps you can format the file that way. For example look at 2GDT.pdb

David

-----Original Message-----
From: biopython-bounces at lists.open-bio.org [mailto:biopython-bounces at lists.open-bio.org] On Behalf Of Peter Cock
Sent: Monday, October 25, 2010 11:33 AM
To: martin djokovic
Cc: biopython at lists.open-bio.org
Subject: Re: [Biopython] writing a PDB----PLEASEEEE HELP

On Mon, Oct 25, 2010 at 4:26 PM, martin djokovic
<martin.djokovic at gmail.com> wrote:
> Hi Peter,
> I want a new PDB with structures A and B superimposed so that I can see them
> both at the same in the same file
>
> So at the end of the simulation/run  I would have A and B (original) and the
> 'ans.pdb' with A as it was but B rotated and translated to be superimposed
> on A in the same PDB
> I want to try this first simple superimposition but actually I want to
> connect A and B together to make a longer strand
> The last residue of A and first residue of B are the same so I can use those
> coordinates to rotate/translate B then connect to A
> I can do that manually using SWISS PDB but I want to do it for many
> structures and its time consuing.

Won't that mean there would be a duplicate residue? i.e. The last residue
of A and first residue of B are the same thing, but would be in the file twice.

Anyway - that basic idea is you must create a Bio.PDB structure object
with both A and B in it (perhaps as two chains in the same model), then
write that to the PDB file. The details depend on how you want to do
the combination - there is more than one way to represent  A and B
in the same PDB file (quite separate from how to do it in Biopython).

Peter

P.S. You could trying writing out two separate PDB files and try simply
concatenating them... it might do what you want.

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