Re: [ccp4bb]: How to make a movie

[Clemens Vonrhein <vonrhein@globalphasing.com>]

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Jeff,

About interpolations: what we did was to use a sliding window (of 9
residues) to get rotation (polar coordinates omega, phi, kappa) and
translation (x, y, z) for each residue between two structures. To
generate intermediate structures you divide the largest kappa value by
e.g. 2 or 4 degree: this gives the number N of intermediate
structures. For each residue you generate the ith of the N
intermediate structures by applying roation (omega, phi, i*(kappa/N))
and translation (i*(x/N), i*(y/N), i*(z/N)). This gives probably a
better path from one structure to the other since it takes rotations
into account.

I'm not sure though, if it will take care of flipped His side chains
etc. And there are still distortions possible ...

For more details: Vonrhein et al. (1995). "Movie of the structural
changes during a catalytic cycle of nucleoside monophosphate
kinases". Structure 3(5),483-490.

The usefulness of these movies is to make static crystal pictures
"alive": the original AK movie was used (at the time) in quite a few
places as a teaching aid in lectures. I found it quite helpful in
noticing smaller, but significant movements: the human eye is probably
smarter than the brain (trying to figure that out from a set of
static pictures and/or coordinates).

Cheers

Clemens

On Fri, Dec 28, 2001 at 04:36:35PM -0500, Jeff Taylor wrote:
> 
> 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.
> 
> In the end, while I think they can be useful is some cases, I don't take
> molecular movies too seriously in their current form.

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