Hi Tomoko,
To print the residue names for each atom just type:
iterate org, print resn
To get the organic small molecules names into a Python list by
molecule, that requires a little effort:
# start a python code block
python
# import stored for passing data back and forth
from pymol import stored
stored.a = []
# create the original selection of all organic atoms
# we'll remove from this list my molecule
cmd.select("allOrg", "org")
# temporary selection
cmd.select("temp", "none")
# while our initial selection is not empty,
# "pop" from it and query the atom's molecule's name
while cmd.count_atoms("allOrg") != 0:
# pop--peek, rather
cmd.select("temp", "first allOrg")
# store the residue name
cmd.iterate("temp", "stored.a.append(resn)")
# remove by molecule
cmd.select("allOrg", "allOrg and not (bm. temp)")
python end
Now, the Python list, "stored.a" has your residue names so,
print stored.a
Cheers,
-- Jason
On Sun, Sep 19, 2010 at 1:15 AM, Tomoko Niwa <tomokon...@gamma.ocn.ne.jp> wrote:
> Dear all
>
>
>
> I want to get resn list of a selection “organic”.
>
>
>
> For example, the list of 2VOM would be [‘HEM’, ‘KLN’, ‘HEM’, ‘KLN’, ‘HEM’,
> ‘KLN’, ‘HEM’, ‘KLN’].
>
>
>
> Any suggestions would be appreciated.
>
>
>
> Sincerely,
>
> Tomoko
>
> ------------------------------------------------------------------------------
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
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