On Wed, Nov 10, 2010 at 8:55 AM, Robert Campbell
<robert.campb...@queensu.ca> wrote:
> So, you need to do:
>
> load this_ligand, all_lig, discrete=1
> load next_ligand, all_lig, discrete=1

Great point, Robert.  In PyMOL when you load without specifying the
discrete flag or set it to zero, any series of states is considered as
one actual object that varies in coordinates (eg. trajectories).  To
save space, PyMOL shares atomic information (except for coordinates).
When we use, "discrete=1" as in
  load myTrajectory.pdb, discrete=1
this makes each state its own object and does not share the atom information.

In Seth's case, it looks like that difference was confusing PyMOL.

Cheers,

-- Jason

On Wed, Nov 10, 2010 at 8:55 AM, Robert Campbell
<robert.campb...@queensu.ca> wrote:
> Hi Seth,
>
> On Tue, 09 Nov 2010 22:54:59 -0500 Jason Vertrees
> <jason.vertr...@schrodinger.com> 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 <set...@gmail.com> 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
> <robert.campb...@queensu.ca>    http://pldserver1.biochem.queensu.ca/~rlc
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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