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

[martin djokovic]

Hello David and everyone else,

Yes David at the moment I am actually doing that-formatting the PDB into 2
models then superimposing them.
Merging the structures when they are in 2 differant PDB files is not
working.
I tried the following:
from Bio.PDB.Model import Model
model1=Model(2ndModel)
structure1.add(model1)
Its not working-I think I might have to better understand the object
"structure"
Is there a better way to merge two structures? Else I will write the 2 pdb
files as models into a single PDB then superimpose.

Another question-maybe some of you use VMD-if I open 1JOY in VMD I can only
see one of the models, I need to scroll using the scroll bar to see the
others-I cannot see them all at once.
So for running the warwick code and seeing its eefect I use RASMOL, is there
a way to look at all the models in the same time without scrolling in VMD? I
prefer VMD to RASMOL so just wondering about that.

Thanks everyone foe all the help.


On Mon, Oct 25, 2010 at 11:49 AM, Lapointe, David <
David.Lapointe at umassmed.edu> wrote:

> 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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