In newer PyMOLs this is as simple as:
print cmd.get_atom_coords(oneAtom)
where 'oneAtom' is an object or selection of one atom in PyMOL.
For example,
load $TUT/1hpv.pdb
print cmd.get_atom_coords("A/30/CA");
-- Jason
On Mon, Mar 22, 2010 at 9:04 AM, Tsjerk Wassenaar <[email protected]> wrote:
> Hi Mohan,
>
> You can use iterate_state, which would be the pymol approach:
>
> coords = {}
> iterate_state 1,n. ca,coords[i]=(x,y,z)
>
> Or you can take a lower level approach; the python one:
>
> for i in cmd.get_model('n. ca').atom:
> print i.coord
>
> cmd.get_model builds you a ChemPy model from a given selection. The
> .atom property is the list of atoms. If you want to know what else is
> possible you might want to have a look at the
> properties/attributes/methods defined:
>
> for i in dir(cmd.get_model('n. ca').atom[0]): print i
>
> Hope it helps,
>
> Tsjerk
>
> Of course neither way would restrict you to plotting...
>
>
>
> On Mon, Mar 22, 2010 at 1:38 PM, mohan raj <[email protected]> wrote:
>> hi all:
>>
>> could any one tell me how to get the coordinates for a specific atom in
>> a particular amino acid using pymol commands....
>>
>> is their a commant with can list the coordinates for each aminoacid in
>> a protein molecule?? \
>>
>> kindly clarify, thanking you in advance.
>>
>>
>> - mohan
>> ------------------------------------------------------------------------------
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> Groningen Institute for Biomolecular Research and Biotechnology
> University of Groningen
> The Netherlands
>
> ------------------------------------------------------------------------------
> 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 ([email protected])
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/[email protected]
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) [email protected]
(o) +1 (603) 374-7120
------------------------------------------------------------------------------
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 ([email protected])
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/[email protected]
