One PARTIAL solution, actually a pretty nice one would be an option in Jmol such as
set interchainbonding ON/OFF
I don't like it, what about chemical cross links, SS bonds, bonds
True, but you would only implement this if you particularly wanted a solution for just this sort of thing, and the suggested "connect all to the oommon C" wouldn't work for the reason that that "common C" would max out with connections. If you had:
set interchainbonding OFF
then you could have that common C actually duplicated in each variable section and the appearance would be just as desired, but the eye would be fooled because there would be two (unconnected) C's there.
Maybe it's a moot point. Joost seems pleased with seeing the rotomer by itself without the rest of the protein. But it's an interesting point I think, that there currently are only a few solutions for displaying the whole protein in animation:
1) creating a file 80x the size, duplicating all other 210 residues each time.
2) implementing "show file" and then recreating the animation file on the fly.
3) implementing "show file" and then generating full models one-by-one, with no animation.
I suppose toying with the PDB format is not a good idea, though. Joost is not creating standard PDB files. Nonetheless, was it ever made possible to display two specific models at the same time? If so, that would obviously be a solution, but I can't remember if you can do that.
Bob
-- Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr
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