Implement Coulombic surface coloring

[pett]

As per summary, also optionally generate a volume data set

[pett]

Tomorrow's daily build will have a 'coulombic' command that works for surfaces whose chain contains only "well known residues" (amino and nucleic acids; some capping groups). A more robust version that works for *any* residues will take much, much longer. Will be working on that.

[Elaine Meng]

Note to the "Phils" is that ChimeraX automatically makes a separate surface for each biopolymer chain, unlike Chimera, which would make one blob containing all the biopolymer chains.

So the "coulombic" command by default will also make separate surfaces per chain, e.g. this gives separate surface models for chains A,B,C,D of hemoglobin:

open 4hhb
coulombic

However, if you need one surface containing all the biopolymer chains, say for 3D printing purposes, it can be done by calculating the surface separately and then specifying it in the coulombic command.

open 4hhb
surface enclose protein
coulombic surfaces #1

Although the surface is actually #1.2 in this case, it might be different for other structures, but it should still be the only existing surface for the atomic model #1 and so you can get away with the broader specification.  This is another reason why it is better for biounit fetches to produce a single model, so you don't have to deal with downstream complexitiies.

If your structure included both protein and nucleic acid and you wanted a single surface enclosing both, it would be something like this with vertical bar for union:

open 6cmn
surface enclose protein | nucleic
coulombic surfaces #1

Probably looks better with just the protein, though.  Also may want to hide other representations that can poke thru the surface:

hide atoms,cartoons

Apologies if this is TMI!  Best,
Elaine

[pett]

Coulombic now also handles non-standard residues (only on Mac right now, soon other platforms).