At 1/17/06, Miguel wrote:
The correct solution is for us to create a new command that allows one to
explicitly insert bonds under script control.
This will sidestep the issue of how 'monitor' should behave.
Hurrah!! This would be great, Miguel. It would solve longstanding problems.
LENGTH
Occasionally it is useful to show a rod that is much longer than a real
bond. Therefore, I vote that the new command be able to show a "bond" of
any length, regardless of chemistry. Hopefully, that would not be a problem.
ENDS
And while we're at it, how will the ends of the bond be specified?
Obviously, one desirable way is to specify two atoms.
However, there are times one wants an arbitrary line or rod whose ends are
not on atoms. Of course, you could insert fake atoms into the PDB file, but
why not enable the bond command to accept x,y,z coordinates as an
alternative to atoms? (Or is there is already a different way to do this?)
Thanks, -Eric
----
Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US
http://www.umass.edu/molvis/martz
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