On Tue, Mar 23, 2010 at 12:48 PM, hari jayaram <hari...@gmail.com> wrote:
> Hi
> I want to write a python/pymol script that will give me residue -residue
> distances within a pdb file programmatically
>
> I know that within pymol I can get a distance object using
>
> select r55 , chain A and resi 55
> select r 22 , chain A and resi 22
>
> distance (r55) ,(r22)
>
> This creates the dist01 object . If I wanted to do this using a python
> script and get a pretty print of all the distances in the distance object ,
> how do I do that?
> Also pointers to other python toolkits that can allow me to make such
> measurements outside pymol will be greatly appreciated.
>
CCTBX will do this for sure - it supports a selection syntax very similar to
PyMOL's. It isn't particularly intuitive, however; if you're interested in
using it, contact me offline and I can send you some examples.
There is also BioPython, which is written for bioinformatics rather than
crystallography and appears to have a much simpler API (but will definitely
read PDB files).
-Nat
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