Re: [PyMOL] on cylindrical helix presentation
1. Make the subunits into separate objects 2. Command set cartoon_cylindrical_helices, on, [object name] for the one you want to have cylinders Shane Caldwell McGill University On Thu, Aug 27, 2015 at 4:01 AM, Smith Liu smith_liu...@163.com wrote: Dear All, Suppose a protein contains 2 subunits. Will you please introduce to me by pymol how to represent helix in one subunit as cylindrical helix, and helix in another subunit as regular helix? Best regards. Smith 夏日畅销榜大牌美妆只要1元 http://r.mail.163.com/r.jsp?url=http%3A%2F%2F1.163.com%2Fhd%2Foneact%2Fhdframe.do%3Fid%3D21%26from%3Dfooter_beautysign=817593681_r_ignore_statId=7_13_79_48_r_ignore_uid=n...@163.com -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] python command to get b-factor and occupancy of a single atom?
Hi Dirk,
cmd.iterate is actually the most efficient function to access atom properties.
If you want a wrapper which directly gets b and q for one atom, it could look
like this (returns a dictionary):
from pymol import cmd
@cmd.extend
def get_signle_atom_props(selection, props=['b', 'q'], quiet=1):
if isinstance(props, basestring):
props = cmd.safe_list_eval(props)
expr = ','.join((repr(k) + ':' + k) for k in props)
expr = '_r.update({' + expr + '})'
r = {}
n = cmd.iterate(selection, expr, space={'_r': r})
if n 1:
print ' Warning: selections spans more than one atom'
if not int(quiet):
print r
return r
You can use the first operator to limit your selection to one atom:
print get_single_atom_props('first polymer')
Cheers,
Thomas
On 27 Aug 2015, at 06:27, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote:
Dear PyMOLers,
I have trouble to find out, which command I could use in a python script
to get the b-factor and occupancy of a single atom.
In the script library, I only found examples getting b-factors iterating
over a selection.
Although, I could iterate over one atom, only, is there a more elegant
way of getting the b-factor and occupancy of a single atom?
Best regards,
Dirk.
--
***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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[PyMOL] off-topic: tenure track faculty position in cryo-EM
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[PyMOL] help making a movie
Dear Pymolers, I am looking forward to make a movie for a nucleic acid where I would like to show the opening/bond breaking of several base pairs and interaction with another protein. Is it possible to do this in pymol? Any help regarding this is highly appreciated! Regards Ravi -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] python command to get b-factor and occupancy of a single atom?
Dear PyMOLers, I have trouble to find out, which command I could use in a python script to get the b-factor and occupancy of a single atom. In the script library, I only found examples getting b-factors iterating over a selection. Although, I could iterate over one atom, only, is there a more elegant way of getting the b-factor and occupancy of a single atom? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] on cylindrical helix presentation
Dear All, Suppose a protein contains 2 subunits. Will you please introduce to me by pymol how to represent helix in one subunit as cylindrical helix, and helix in another subunit as regular helix? Best regards. Smith-- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
