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

[martin djokovic]

João and Peter,

I think I have confused everyone by bringing in my second problem.
This is what I really want to do now
I have 2 PDB files protein1.pdb and protein2.pdb
(I have stopped using A and B as people assume its chain A and B NO they are
not I just called them A.pdb and B.pdb for
convinience )

Both ptotein1.pdb and protein2.pdb have the same residues and I want to
superimpose protein2.pdb on protein1.pdb
Once I have rotated and translated the coordinates of protein2.pdb I want to
write a 3rd PDB file containing the coordinates of protein1.pdb and the
tras/rotated coordinates of protein2.pdb thats all.
Thank you
Martin

On Mon, Oct 25, 2010 at 12:09 PM, João Rodrigues <anaryin at gmail.com> wrote:

> Dear Martin,
>
> To write a new PDB file you first must ensure that there are no naming
> clashes. This means that you can't have two chains named A, nor two residues
> numbered 12 in the same chain for example.
>
> For your particular problem, I'd suggest the following:
>
> Renaming the first (reference) structure chains to start from A. Then
> rename the following structures chains accordingly.
>
> Try for example using a combination of a for loop with the Python chr
> function (A character is ord 65). Very crudely:
>
> i_chain = 65
> for structure in list_of_structures:
>   for chain in structure:
>     chain.id = chr(i_chain)
>     i_chain += 1
>
> This should fix your chain problems. Afterwards, all you need is to combine
> all your chains in ONE structure object. I believe it to be easier.
>
> Just add your structure B information to your structure A information. Check
> the documentation<http://www.biopython.org/DIST/docs/cookbook/biopdb_faq.pdf>on how to manipulate SMCRA objects.
>
> This will yield you a final structure object with both structure A and
> structure B which you can then output and save.
>
> Hope it helps! Best!
>
> João [...] Rodrigues
> http://doeidoei.wordpress.org
>
>
>
> On Mon, Oct 25, 2010 at 5:59 PM, 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
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>