Re: [PyMOL] Rigimol

[Warren D. <wa...@de...>]

Colin,

Unfortunately, that is hard to do:  there is no guarantee that the
proposed (characteristic) path of motion which relates any two spacial
orientations will possess reasonable chemistry or sterics.  RigiMOL does
make an attempt to resolve simple conflicts, and the refinement step can
address minor local violations, but that is about it.

The only way to work around this problem is to manually create one or
more artificial intermediate conformations which do not exhibit such
clashes and then morph conformation 1 to the first artificial
conformation and then morph the last artificial conformation to
conformation 2.  That can be a lot of work, and it kind of misses the
point:

PyMOL (rigimol) structure morphs are only intended for visual comparison
of two or more experimentally-determined structures.  Molecular morphs
are not (and should not be portrayed as) energetically-reasonable
physiochemical paths of interconversion.

To rigorously identify reasonable (low-energy) paths of interconversion,
one must instead employ steered molecular dynamics or biased monte carlo
simulations.  Those are compute-intensive processes well beyond PyMOL's
capabilities.

Cheers,
Warren

> -----Original Message-----
> From: Colin Levy [mailto:c....@ma...]
> Sent: Thursday, September 10, 2009 8:59 AM
> To: pym...@li...
> Subject: [PyMOL] Rigimol
> 
> Hi,
> 
> I have generated a morph between two large scale domain motions using
> Rigimol . The output is fine except that the two domains pass through
> each other during their trajectory. Anyone know how to avoid this type
> of problem.
> 
> Thanks
> 
> Colin
> 
>
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