[chimera-dev] Chimera stuff

[Elaine Meng]

  Hi Ed,
You're welcome!

>* Why can you "surface ligand", but not "select ligand"?

Most commands accept an atom specification, but ligand/main/etc. are
surface categories, not atom specs.  Of course, that is just a 
restatement of your observation that "ligand" does not work as an
atom spec.  The surface categories were developed since there needed
to be reasonable groupings for surface calculation, a whole different
issue than whose surface is actually displayed.  For example, if
you surface a molecule such as biotin that is considered "ligand," the
surface actually encloses the biotin, but if you surface some random
residue in the protein, Chimera "knows" it is part of "main" and only
shows surface where the residue is at the surface of the main protein.
Thus surface *creation* would use the categories, but then *display*
of the surface could use either categories as a whole, or atom specs,
which could be subparts of categories.

When using all those commands that use atom specs, I agree it might
be convenient to also allow ligand/main/etc. to be atom specifications.
The programmers on the team would need to think about this a bit more,
in case there are ramifications.  For now, you could use the atom spec
          @/surfaceCategory=ligand

>* Automatic chain break detection would be really helpful.  Currently, 
>Chimera connects all the residues in a chain, even when it's clear from the 
>bond length that there must be a chain break.

Check out the command "longbond" - it should do the trick.  There should not
be a lot of long bonds in PDB standard-compliant files.  They will occur
in segments of missing density, but their presence does inform you that
there is no chain break in reality, just missing density.  Also, it is
pretty easy to just use longbond if you want them to go away.  The
command can take parameters, but in practice I have never needed to
specify them; I just use "longbond" with no arguments.

Hope this helps!
  Elaine
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Elaine C. Meng, R.Ph., Ph.D.
Babbitt Lab and Computer Graphics Lab
meng at cgl.ucsf.edu
http://www.cgl.ucsf.edu/home/meng/index.html
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