If you have a PDB file of the ligands and know the number of atoms in
each ligand, then you could introduce a TER card after the each ligand.
That way PyMOL will not draw bonds between the ligands. If you want to
visualize it one after the other then MODEL and ENDMDL cards before and
after each ligand would work too.
-Kaushik
On Tuesday, August 17, 2004, at 01:02 PM, Michael George Lerner wrote:
Hi,
I have a file which contains a protein and a bunch of ligands. The
ligands come from a Monte Carlo simulation where they were allowed to
talk
to the protein, but not to eachother. So, lots of the ligands overlap.
When PyMOL sees this, it draws bonds between the ligands. Every time I
load up one of these structures, I have to unbond things with something
like
for i in range(160,660):cmd.do('unbond resi %s, not resi %s'%(i,i))
which takes a *really* long time. Is there a faster way to do this? I
once hacked up the PyMOL source so that HETATMS with resi > N didn't
get
bonded to anything else in the first place, but that's obviously a bad
way
to do things (and I can't seem to compile things myself on our SGIs, so
it doesn't work there anyway).
Thanks,
-michael
--
This isn't a democracy;| _ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
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