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 <mohanrajdec2...@gmail.com> 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
------------------------------------------------------------------------------
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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
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