Re: [ccp4bb]: How to make a movie

[Edward Berry <eaberry@lbl.gov>]

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Jeff Taylor wrote:
> 
> Edward Berry wrote:
> >
> > That sounds almost too simple. Are bond lengths/angles preserved during
> > the morph? if a Histidine rotated 180* about CHI2, wouldn't the NE1 and
> > CE2 atoms pass through each other on the way to their new positions?
> > Do any morphing programs preserve bond lengths and angles during the
> > morph? Perhaps one could express the structure in terms of dihedral
> > angles and interpolate linearly between the starting and final values
> > for the dihedral angles. Still in the case of large-scale movements
> > you might get one domain passing through another on the way to its
> > final position, where in nature it makes a two-stage movement to go
> > around.
> >
> > ed
> 
> Yes it is too simple.  I just make a linear interpolation between the
> old and new coordinates.  This doesn't preserve any physical aspects of
> the molecule and the intermediate structures can be severely mangled.  A
> 180 degree rotation of a Histidine (or tyrosine, phenylalanine, etc.)
> will look really funny.  To make a physically reasonable morph one would
> need to employ some kind of directed molecular dynamics, or at least
> incorporate some kind of energy minimization for the intermediate
> steps.  What a mess.  On the bright side, the linear interpolations
> often work quite well, provided that the motions aren't too large or
> complex, AND they aren't taken too seriously.
> 

yes, I can see that for rotations of 10-20 degrees the linear interpolation 
would be a good approximation - the distortion would not be discernible.
and this would be the case for the majority of conformational changes 
observed in different crystal structures. Sorry for nit-picking.

Still I'm curious if there are slightly more sophisticated approaches 
that don't take as much CPU-time or know-how as directed molecular dynamics
a la Izrailev et al. (Biophys J 1999 77:1753-68 Steered molecular dynamics 
simulation of the Rieske subunit motion in the cytochrome bc(1) complex.)
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10512801

Ed