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

[martin djokovic]

Thanks Peter but if I just want to superimpose A and B and get a 3rd PDB
file that shows A and B superimposed how do I do it?
Following the method I did (first post) just makes me a copy of A as the 3rd
file-I cant still figure out what happened to the result of the "apply"
command that should have rotated and translated the coordinates of B to
superimpose them on A.
I want to write the result (now haveing A and superimposed B) into a 3rd
file.
Not sure if you are understanding my question due to my poor explantion of
the problem-I am sorry about that.
Imagine if 1JOY only has 2 strucutres instead of 21 and they are 1JOY-A and
1JOY-B how do I superimpose them and get 1JOY-C that shows them nicely
overlapping as in the final output in your warwick example?
Thanks once again,
Martin

On Mon, Oct 25, 2010 at 11:59 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Mon, Oct 25, 2010 at 4:36 PM, martin djokovic
> <martin.djokovic at gmail.com> wrote:
> > 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
>
> The example on my Warwick page uses a single PDB file containing
> multiple models, but you can superimpose two separate PDB files with
> Biopython.
>
> You (apparently) are stuck at a different task - combining two PDB
> files into one. You need to be careful about not creating a bad PDB
> file where residues or chains are multiply defined (e.g. if both your
> structures are called Chain A in Model 1).
>
> Peter
>