Re: [PyMOL] coordinates

[Jed G. <jgo...@wh...>]

Of course, you could just use the .pdb file as a text file:

grep CA xxxx.pdb | cut -f 2,4,7,8,9

will get you the amino acid number, the amino acid identity, and x,y,z 
coordinates for the CA.

Jed

Jason Vertrees 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
>
> 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
>>
>> ------------------------------------------------------------------------------
>> Download Intel&#174; 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
>> _______________________________________________
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>>
>>     
>
>
>
>   

-- 
------------------------
Jed Goldstone
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS#32
Woods Hole, MA 02543
http://www.whoi.edu/hpb/Site.do?id=481
Phone: 508-289-4823