Re: [PyMOL] Centering multiple ligands

[Thomas H. <tho...@sc...>]

Hi Meginir,

there are several "center of mass" scripts on the PyMOLWiki. If you have
PSICO installed, try this:

python
sele = 'yourobject'
cmd.alter(sele, 'q=1') # SDF files load with q=0
for i in range(1, cmd.count_states() + 1):
  cmd.alter_state(i, sele, '(x,y,z)=(x-%f,y-%f,z-%f)' %
tuple(psico.querying.centerofmass(sele, i)))
python end

Cheers,
  Thomas

meginir urestal wrote, On 04/23/14 05:15:
> Hi,
> 
> I have an sdf file with several ligands. The problem I am facing is that
> each of the ligands is in a different patch of space. Does anyone know
> of a way to center all the ligands around the same point for easy viewing?
> 
> Thanks,

-- 
Thomas Holder
PyMOL
Schrödinger, Inc.