Re: [ccp4bb]: How to make a movie

[Jeff Taylor <jstaylor@duke.edu>]

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Hello Steve -

Thanks for pointing out the Young et al. paper.  I hadn't noticed it
previously, as Cell(!) is generally not the place I look for MD papers. 
I have also tried some directed molecular dynamics for the purpose of
making a movie of a DNA polymerase structure that we are working on.  My
modifications to CHARMM for directing the dynamics were perhaps not as
sophisticated as those used by Young et al., but the results were very
reasonable.   

The code I offered up on the ccp4bb was for making trivial movies with
as small a time investment as possible.  While very simplistic, it has
the advantage of not masking its limitations behind good
stereochemistry.

In evaluating the usefulness of the resultant movies so far I find that
linear interpolations, while chemically ugly, reveal protein motions
just as well as the MD approach and do so with much less time invested. 
The MD approach is also risky in that if it looks too good, the eye
gives equal weight to calculated intermediate structures and the
experimentally determined end points, which could be quite misleading.

Jeff Taylor

-- 
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Dr. Jeffrey S. Taylor       Duke University Medical Center
Department of Biochemistry  Box 3711, Nanaline Duke Bld  
Phone (919) 681-5266        Durham, NC 27710



"Soisson, Stephen Michael" wrote:
> 
> 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
>