On 19 December 2011 19:54, David Lonie <lonieda...@gmail.com> wrote: > On Mon, Dec 19, 2011 at 2:17 PM, Geoffrey Hutchison > <ge...@geoffhutchison.net> wrote: >>> Is there currently a GUI-based method to generate and view >>> conformations of a molecule? Using the forcefield extension, I appear >>> to be generating the conformers, but in View > Properties > Conformer >>> Properties, only a single entry shows up. >> >> What conformer search are you using? The weighted search will just give you >> the lowest energy conformer, not generate new ones. Systematic searching >> should give you a set. > > Even with systematic and random search, I only get a single conformer > in the properties dialog. Is this a bug or am I missing a step? > (avogadro master and OB trunk)
At some point I changed the behaviour of systematic search to match the weighted search. This was (a) for consistency, and (b) because the systematic search uses up your memory if the molecule has several rotatable bonds. Sorry if this was a mistake, but it seemed that the goal of the systematic search was simply to find a single low energy conformer. >>> We would like to do this as part of a lab, so we need a GUI-based, >>> student-friendly way to generate and compare conformations. Does >>> anyone know if such a workflow is possible using existing tools? >> >> Without much coding, yes. Open Babel has a new (v2.3) conformer search >> framework, which should probably replace the weighted search and will >> generate multiple conformations. Better yet, you can either pick low-energy >> conformers, or a diverse set (i.e., maximizing RMSD differences). >> >> I just haven't had time to splice the new framework into the forcefield >> extension. > > I should be able to spend some time on this, since it will be related > to my PI's lab course. I saw a GA search heuristic go into trunk, is > this the one you mean? I can replace the current weighted search in > the forcefield extension with that. Are the different fitness options > already incorporated into OB, or can it take a user supplied fitness > function callback? I can add some of these in if there's time. > >> I also have some ideas about manual dihedral scans, but that will need >> someone with more programming time. > > Check out the RotateSelection extension example > (libavogadro/examples/thirdPartyExtensions/04-RotateSelection), I > think it should be able to do dihedral scans without too much trouble, > you might be able to modify that for a quick version. > > Dave > > ------------------------------------------------------------------------------ > Learn Windows Azure Live! Tuesday, Dec 13, 2011 > Microsoft is holding a special Learn Windows Azure training event for > developers. It will provide a great way to learn Windows Azure and what it > provides. You can attend the event by watching it streamed LIVE online. > Learn more at http://p.sf.net/sfu/ms-windowsazure > _______________________________________________ > Avogadro-Discuss mailing list > Avogadro-Discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/avogadro-discuss ------------------------------------------------------------------------------ Learn Windows Azure Live! Tuesday, Dec 13, 2011 Microsoft is holding a special Learn Windows Azure training event for developers. It will provide a great way to learn Windows Azure and what it provides. You can attend the event by watching it streamed LIVE online. Learn more at http://p.sf.net/sfu/ms-windowsazure _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
