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 ------------------------------------------------------------------------------ The Next 800 Companies to Lead America's Growth: New Video Whitepaper David G. Thomson, author of the best-selling book "Blueprint to a Billion" shares his insights and actions to help propel your business during the next growth cycle. Listen Now! http://p.sf.net/sfu/SAP-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
