Hari,
> I want to write a python/pymol script that will give me residue -residue
> distances within a pdb file programmatically
In PyMOL, this is easy to program. Here's a small script to give you
all pairwise distances of the atoms in residue 30 of chain A of 1hpv:
import pymol
from pymol import stored
fetch 1hpv, async=0
remove not (i. 30 and c. A)
orient
stored.ids = []
iterate_state 1, 1hpv, stored.ids.append(ID)
python
for x in stored.ids:
for y in stored.ids:
print "Dist from atom ID %d to %d = %f" %
(x,y,cmd.get_distance( "ID
%s" % x, "ID %s" % y))
python end
Doing this from a script is easy. Doing this from extant distance
objects is not.
Cheers,
-- Jason
On Tue, Mar 23, 2010 at 3:48 PM, hari jayaram <[email protected]> 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.
> Thanks for your help
> Hari
>
>
> ------------------------------------------------------------------------------
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) [email protected]
(o) +1 (603) 374-7120
------------------------------------------------------------------------------
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Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
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http://p.sf.net/sfu/intel-sw-dev
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