Re: [PyMOL] small molecule geometry gets whacked in creating multi-state object. rebuild?

[Robert C. <rob...@qu...>]

Hi Seth,

On Tue, 09 Nov 2010 22:54:59 -0500 Jason Vertrees
<jas...@sc...> wrote:

> Hi Seth,
> 
> I haven't seen that (in this scenario).  Can you send me a few PDB examples?
> 
> Cheers,
> 
> -- Jason
> 
> On Mon, Nov 8, 2010 at 10:13 PM, Seth Harris <se...@gm...> wrote:
> > Hi all,
> > I feel I should know this one. I have a program looping through structures
> > and bringing each small molecule into a single multi-state object so I can
> > tab through the states.
> > I do:
> > create all_lig, this_ligand, 1, 1
> > then go on to the next one:
> > create all_lig, next_ligand, 1, 2
> > and so on....
> > however, the bonds get all messed up, presumably with atom names
> > confused? I tried issuing a "rebuild all_lig" in between adding but that
> > didn't seem to help. What am I missing?

It sounds like you are loading a set of *different* structures into the
multi-state object.  I don't think you can do this properly with the
"create" command.  I think the only way to do this and retain the correct
bonding information is to use the load command directly with the "discrete=1"
option.

So, you need to do:

load this_ligand, all_lig, discrete=1
load next_ligand, all_lig, discrete=1

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc