Re: [ccp4bb]: Structural Transition

[Richard Gillilan <reg8@cornell.edu>]

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>
> > Hi, All,
> >
> > Is there a program that can make a movie of a protein structural
> > transition, given a "start" and an "end" conformations of the same
> > protein?
> >

I recently did a fairly complex cartesian-space interpolation between
multiple structures with different numbers and types of atoms using
OpenDX (www.opendx.org). This may be of use if, for example, you find
that a covalently-bound Oxygen is replaced by a crystallographic water and you want to
animate the change. We also animated movements in crystallographic
waters. The process was tedious, but could be done. I suspect lsqman is
an easier solution in cases where you are only interested in conformational
changes of a single structure rather than chemical changes.

Another alternative is to use Ron Elber's method of finding
paths of minimum energy on the potential surface by minimizing
an unusual action functional. You can specify starting and ending
states and in initial guess for the path (often a line).  This method
takes you a step beyond lsqman in that an empirical forcefield is used.
You should be able to get the code from Ron through the NCRR at Cornell: http://www.tc.cornell.edu/Research/Biomed/index.asp


Richard Gillilan
MacCHESS
Cornell


> > We have determined two very different structures of one protein domain,
> > and would like to present the structural transition in a reasonable way.
> > Going from one structure to the other may involve unfolding part of the
> > protein and refold it. Such a big conformational change is difficult to
> > model, therefore, a program with some level of automation would be really
> > helpful.
> >