Hi Sean,
try the attached example script, hope you manage to modify it for your
needs.
Cheers,
Thomas
Sean Law wrote, On 02/08/12 19:34:
Takanori,
I've tried the following:
for a in range(1,8): cmd.mdo(a,"hide sphere; select test,
input_object_name & c. b & i. 19 around 4 & resn HOH; show sphere, test")
where "HOH" is the residue name for water (so I want to know only the
waters within a 4 Angstrom radius of residue number 19).
However, this command keeps selecting the same atoms for every frame and
shows them as spheres even if they have moved beyond the 4 Angstroms.
Am I using the wrong selection logic here? Again, I only want to see
the water atoms within 4 Angstroms of residue 19 for any given frame.
Thanks in advance.
Sean
> Date: Wed, 8 Feb 2012 11:06:21 +0900
> From: t.nak...@mail.mfour.med.kyoto-u.ac.jp
> To: magic...@hotmail.com
> CC: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Update Selection From Frames
>
> Hi Sean,
>
> > I was wondering if it were possible to have a selection update
itself for every frame.
>
> You can use mdo command for that.
>
> http://www.pymolwiki.org/index.php/Mdo
>
> Best regards,
>
> Takanori Nakane
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
'''
Show water atoms within some radius of a reference atom during a movie.
'''
from pymol import cmd
obj = 'myobj'
natoms = 50
# create water
for i in range(natoms):
cmd.pseudoatom(obj, pos=[i*3,0,0], resn='HOH', name='O', elem='O', resi=i)
# create reference atom
cmd.pseudoatom(obj, pos=[0,3,0], resn='CL', name='CL', elem='CL', resi=1000)
# generate states
for state in range(2, 3*natoms):
cmd.create(obj, obj, 1, state)
cmd.alter_state(state, 'last ' + obj, 'x=state-1', space=locals())
# selections
cmd.select('ref', obj + ' and resi 1000')
cmd.select('test', 'none')
cmd.disable('test')
# function to call during movie
def callback(state):
cmd.hide('spheres')
cmd.select('test', 'ref around 10 and resn HOH', state=state)
cmd.show('spheres', 'test')
# make movie
cmd.mset('1-%d' % cmd.count_states())
for state in range(1,cmd.count_states()+1):
cmd.mdo(state, "callback(%d)" % (state))
# show and play
cmd.show_as('nonbonded')
cmd.orient()
cmd.mplay()
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