Re: [ccp4bb]: Structural Transition

[Tsan Xiao <xiao@chop.swmed.edu>]

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Hi! All,

Thank you for those who responded to my inquiry about making a movie for
structural transition. Here is the summary:  

Holly Jing and Gerard Kleywegt suggested the morph server @
http://bioinfo.mbb.yale.edu/MolMovDB/, which seem to be very easy to use
if you read the references;

Several alternatives were also suggested by Gerard Kleywegt and Richard
Gillilan, such as Lsqman @ http://xray.bmc.uu.se/usf/mol_morph.html;  
and OpenDX @ http://www.opendx.org (an artistic program, basically);  
or Ron Elber's method @ http://www.tc.cornell.edu/Research/Biomed/index.asp. 
(You would have to ask for the code and instructions)

Prof. Edgar Meyer actually may have some "secret weapons" if one is
interested in investigating (re)folding trajectory in more details :-)

The morph server @ yale seems to be easier to use. However, I had some
trouble getting results, probably due to the fact that some serious
unfolding is involved in my case. The authors have been notified about the
problem and hopefully they are trying to fix it. Haven't tried other
programs yet. As s-ramaswamy cautioned, this kind of "movie" will need
more justification as to its biological relevance. Our purpose of making
such a movie is just to show the magnitude of the structural changes.

Thank you again for your replies.

---------------------------------------------------
Tsan Xiao, Ph.D.
Howard Hughes Medical Institute
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Dallas, TX 75390-9050
Tel: 214-648-5039
Fax: 214-648-6336
Email: xiao@chop.swmed.edu