I enjoyed reading the transcript of the latest BioMOO. I have only
one postscript to add. With regard to Clare Sansom's question about making
a molecular dynamics (MD) movie, I'd like to suggest that you take a look
at an exciting MD animation showing thermal motion and partial unwinding of
an alpha helix segment made by Raul E. Cachau (cachau@ncifcrf.gov). This
can be viewed with Xmol from the Rzepa/Whitaker hyperactive molecules site
http://www.ch.ic.ac.uk/hm_second.html. Tim Maffett of MDLI used this
example obtained from the Imperial College site to implement XYZ animation
display in Chime, which is free for adacemic and personal use at home (and
will remain so indefinitely).
Although this MD animation has not yet made it onto MDLI's 'cool examples'
page, Tim kindly provided it to me and gave me permission to share it with
you. You can download Chime from www.mdli.com (installation is extremely
simple) and then use Netscape to view
http://www.umass.edu/microbio/rasmol/private. BE WARNED that there was a
bug in the Chime released in May (at least for Windows 3.1) which caused it
to stop working a month before the announced July 31st. You can get a more
recent version from MDLI which fixes this. Unfortunately, the more recent
version has a new bug which corrupts the top portion of the image.
Nevertheless, you can see enough of the animation to see what will be
possible with Chime. I particularly recommend changing the display of the
bottom image of 'alpha helix unfolding' to spacefill. (Click the right
mouse button, or on Macs, hold down the button, till the familiar
RasMol-like menu appears.) I have sent an email inquiry to Raul Cachau
asking how this XYZ animation was constructed, but have not received a
reply.
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Eric Martz, Professor of Immunology emartz@microbio.umass.edu
Molecular visualization (free!): http://www.umass.edu/microbio/rasmol
Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs
Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology
Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578
Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720
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