Re: [PyMOL] Get number of residues in model

[Tsjerk W. <ts...@gm...>]

Hi Martin,

Here's a fourth option (and the technique worth noting :p ):

print len( set( [(i.chain,i.resi,i.resn) for i in
cmd.get_model(selection).atom] ) )

Cheers,

Tsjerk

On Tue, Nov 29, 2011 at 4:26 PM, Jason Vertrees
<jas...@sc...> wrote:
> Hi Martin,
>
> You get three options:
>
> (1) You can count alpha carbons:
>
> fetch 1rx1, async=0
>
> count_atoms n. CA
>
>
> (2) But, a protein could be missing alpha carbons then this is more
> complete (and the technique worth noting):
>
> n=0
> select qq, polymer
> select pp, None
> python
> while cmd.count_atoms("qq"):
>  cmd.select("pp", "br. first qq")
>  cmd.select("qq", "qq and not pp")
>  n+=1
> python end
> print "count_atoms: %d" % n
>
> If you put:
>
> select qq, *
>
> you'll get a higher count (160) because one atom in 1rx1's inorganic
> set is also named "CA".
>
>
> (3) The shorter version of (2) is:
>
> print len(cmd.get_model("poly").get_residues())
>
> Cheers,
>
> -- Jason
>
>
> On Tue, Nov 29, 2011 at 9:50 AM, Martin Hediger <ma...@bl...> wrote:
>> Dear List
>> How can I compute the numbers of residues in a model?
>>
>> Martin
>>
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>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands