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

[martin djokovic]

So if we just focus on superimposing A and B for now-
Are you saying its impossible to do it while A and B are seperate PDB's?
They should be in the same PDB?
Ok like the example in the warwick university site for 1JOY?? Oh I see-I
thought that I could do the same thing but do it for 2 seperate
PDB's--please confirm this.
I was really getting confused as I tried to follow that as much as possible
but do it using 2 files

On Mon, Oct 25, 2010 at 11:32 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> 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.
>