Re: [PyMOL] Getting information fron selected objects

[Daniel S. <ds...@gw...>]

Hi Phil,

one option to get access to the coordinates is using the chempy model of a 
given selection ( named "(sele)" if you clicked it).

m = cmd.get_model("(sele)")

the chempy model contains a list of atom objects which contain most properties 
you might need.

for atom in m.atom:
     print atom.id, atom.name, atom.resn, atom.resi, atom.coord

To extract the coordinates of all atoms you can simple do:

coords = map(lambda a: a.coord, m.atom)

or if you need the coordinates as numpy arrays use:

from numpy import *
coords = map(lambda a: array(a.coord), m.atom)

gives you a list of numpy arrays

or:
coords = matrix(map(lambda a: a.coord, m.atom))

will produce a numpy matrix with your coords.

Then you might do whatever you want with the coordinates and update the 
coordinates of the chempy model.
As far as I now, you can not transfer them back easily to PyMOL but you can do 
a little trick.

Load the modified model as new pymol object:

cmd.load_model(m,"modified")

and then update the original selection with the coords from the modified 
object.

cmd.update("(sele)","modified")

Then you can delete the modified object.
cmd.delete("modified")

Cheers,
Daniel





On Tuesday 19 January 2010 08:00:51 pm Phil Payne Local wrote:
> I am writing a Pymol plugin, in which I need to extract, manipulate, and
> replace the coordinates of selected atoms.  Are there examples out there
> I could use as a prototype?
> 
> For starters, what command(s) do I use to get the name strings of
> residues that I've selected with mouse clicks.  I would like to assign
> these to a variable.
> 
> Then the same question applies to coordinates.  How do I assign the
> values of atomic coordinates to a list variable in my plug_in script?
> 
> 
> ---------------------------------------------------------------------------
> --- Throughout its 18-year history, RSA Conference consistently attracts
>  the world's best and brightest in the field, creating opportunities for
>  Conference attendees to learn about information security's most important
>  issues through interactions with peers, luminaries and emerging and
>  established companies. http://p.sf.net/sfu/rsaconf-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
> 

-- 
Dr. Daniel Seeliger
Computational Biomolecular Dynamics Group
Max-Planck-Institute for Biophysical Chemistry
Tel. +49 (0) 551-201-2310
http://wwwuser.gwdg.de/~dseelig