[PyMOL] coords

[mohan r. <moh...@gm...>]

hi Jason:

thank you so much.... your
print cmd.get_atom_coords("A/30/CA");

command is working fine!!!

i wish to know how to edit the coordinates and change the position of the
atom.....

when i open the pdb file in the word document i could see all the
coordinates.. is it possible that i can change the coordinates their
itself?????  further the command line you have stated give the coords for
the entire amino acid.... is it considering all the atom in the aminoacid
and giving the coords for the central value????

-mohan

jason wrote:

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
- Show quoted text -
On Mon, Mar 22, 2010 at 9:04 AM, Tsjerk Wassenaar <ts...@gm...> 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 <moh...@gm...>
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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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC