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RE: [ccp4bb]: How to make a movie
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Another approach for morphing from one conformation to another is to use
targeted molecular dynamics, as described in:
Young et al. (2001) Cell 105:115-126.
On page 121, there is a method described to generate an animation of the
activation loop of a Src family kinase. They use a starting structure
(inactive) and a target structure (active) with an artificial energy term
related to the rms deviation from the target structure. The conformation of
the loop is not dictated during the simulation, but it has the advantage
that it will obey all of the bond, angle, electrostatic, etc. energy terms
that you put in the simulation. They state that 0.1 ns of simulation will
do they trick. I have seen Matt Young and John Kuriyan show these
animations in a talk and they are very smooth and quite nice. I am sure
that they could help you with the specifics of the technique if anyone is
interested.
Hope this helps.
Steve
---------------------------------------
Stephen M. Soisson, Ph.D.
X-ray Crystallography (E & C.B.)
Merck Research Laboratories
Phone: (732)594-4349
-----Original Message-----
From: Clemens Vonrhein [mailto:vonrhein@globalphasing.com]
Sent: Saturday, December 29, 2001 9:16 AM
To: Jeff Taylor
Cc: CCP4 Bulletin Board
Subject: Re: [ccp4bb]: How to make a movie
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*** CCP4 home page http://www.ccp4.ac.uk ***
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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