[Chimera-users] Rapid residue identification near ligands

[Elaine Meng]

Greetings Korbin,

That “smart initial display” makes use of Chimera’s automatic initial classification of atoms into ligand, ions, solvent, and main.  The rules for identifying those groups are outlined here, but you can just make use of it in Chimera by specifying “ligand” in various commands:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html#surfcats>

Note, however, that rules can only go so far, and “ligand” will often include things like sulfate, phosphate, glycerol, etc. that may be included in the crystallization experiment, but are not necessarily biologically relevant.

As for contacts, the smart initial display is very similar to the ribbons preset described here
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#interactive>
… in that they show residues within 3.6 A of “ligand” or “ions”

You could choose to define contacts with a different cutoff, either a simple distance between atomic centers (as in command-line zone specifications) or amount of VDW overlap, which takes into account the different sizes of different atom types (as in the “findclash” command).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

Examples:

select ligand z<4.5
writesel ~/Desktop/contacts1.txt
   …select all residues with any atom within 4.5 A of “ligand” (which includes “ligand”), write list of selected residues to file

color red ligand z<4.5 & protein
   …color red protein residues with any atom within 4.5 A of “ligand”

findclash ligand test protein overlap -0.5 hb 0 select true log true
     …select all ligand-protein atom pairs with VDW surfaces within 0.5 A of each other and write pair information to Reply Log

For scripting looping through several structures, see <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Aug 31, 2015, at 7:31 PM, Korbin West <khwest16 at wabash.edu> wrote:
> 
> Greetings all,
> 
> We need to be able to easily assign ligands to a chain (or chains) and to rapidly ID the residues in contact with it. I believe Chimera processes the structures and immediately displays ligands and maybe contacts, so it "knows" this information somehow. Does anyone know of a way to identify these easily and quickly so we can analyze large numbers of files? Also, if the output could be in the form of a text file or such that would be beneficial as well. Thank you all for your help. 
> 
> Best,
> Korbin West
> Wabash College