From: hari j. <ha...@gm...> - 2010-03-23 19:48:27
|
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 |
From: David H. <li...@co...> - 2010-03-23 20:04:05
|
PyMol doesn't provide programmatic access to actual bond objects. Instead, you have to do what was suggested 5 days ago: http://www.mail-archive.com/pym...@li.../msg07745.html -David On Tue, Mar 23, 2010 at 3:48 PM, hari jayaram <ha...@gm...> 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 > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: hari j. <ha...@gm...> - 2010-03-23 20:35:53
|
Thanks a tonne David and Nathaniel, The script in that post <http://www.mail-archive.com/pym...@li.../msg07745.html>is exactly what I was looking for. I may also give cctbx.python a try , If I remember right phenix, cns and xplor use a similar kind of selection syntax which as Nat said is not too different from pymol given its roots. Thanks again Hari On Tue, Mar 23, 2010 at 4:03 PM, David Hall <li...@co...> wrote: > > PyMol doesn't provide programmatic access to actual bond objects. > Instead, you have to do what was suggested 5 days ago: > > http://www.mail-archive.com/pym...@li.../msg07745.html > > -David > > On Tue, Mar 23, 2010 at 3:48 PM, hari jayaram <ha...@gm...> 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 > > > > > > ------------------------------------------------------------------------------ > > Download Intel® Parallel Studio Eval > > Try the new software tools for yourself. Speed compiling, find bugs > > proactively, and fine-tune applications for parallel performance. > > See why Intel Parallel Studio got high marks during beta. > > http://p.sf.net/sfu/intel-sw-dev > > _______________________________________________ > > PyMOL-users mailing list (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > > |
From: Nathaniel E. <nat...@gm...> - 2010-03-23 20:14:21
|
On Tue, Mar 23, 2010 at 12:48 PM, hari jayaram <ha...@gm...> 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 |
From: Jason V. <jas...@sc...> - 2010-03-23 21:22:09
|
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 <ha...@gm...> 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 > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |