Thanks Robert and Jason

Indeed, I have different small molecules as Robert surmised and subsequent ones affect the connectivity of the earlier ones (and representations for some reasons, colors and spheres, etc. become unpredictable) when using the create command. I had noted that "discrete" flag for the load command, but not having separate files from these aligned in the right spot is there really nothing similar to do on the fly without saving out the newly aligned (using the surrounding protein) and extracted ligand into its own pdb file and loading that back in again with the discrete flag on? That will work, but seemed a bit clunky!

Thanks again for the tips to that functional route!


Hi Seth,

On Tue, 09 Nov 2010 22:54:59 -0500 Jason Vertrees
<> 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 <> 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"

So, you need to do:

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


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