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 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, R.Ph., Ph.D. Babbitt Lab and Computer Graphics Lab meng@cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=