I'm a little confused by what PDB assemblies you are talking about that are distributed as multi-state structures, but assuming they are similar to NMR models... you can use intra_fit ( http://www.pymolwiki.org/index.php/Intra_fit )
For example, with 2kgx, we start out with chain a in state 1 and 2 and having an rms of 0.927 and chain b having an rms of 1.143 intra_fit 2kgx and chain a now, chain a has an rms of 0.923 and chain b has an rms of 1.155 intra_fit 2kgx and chain b now, chain a has an rms of 0.952 and chain b has an rms of 1.130 Note, it can take a target state, that all other states are aligned to, etc. On Wed, Nov 5, 2014 at 5:23 AM, Spencer Bliven <sbli...@ucsd.edu> wrote: > Hey, I've been doing a lot of work with PDB assemblies, which are > distributed as multi-state structures. I would like to be able to align > them based on individual chains from individual states. However, I haven't > been able to figure out any way to uniquely identify atoms by state. > > The select statement contains a `state` parameter, but as noted in this > 2010 thread > <https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg08224.html> > it doesn't seem to do anything. The thread also suggests using > cmd.get_model(), but I'm not sure how to get a selection based on a > chempy.models.Indexed instance. > > My current workaround is to split_states, use alter to make all the chains > unique, then merge the structures again. This is incredibly tedious. Does > anyone know a better way? > > It would be nice if (1) the select command were fixed, and/or (2) add a > property selector for states. > > Cheers, > Spencer > > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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 >
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