[Chimera-users] Overlay binding sites

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 28 17:06:18 PST 2013

Hi Markus,
Not sure exactly what you mean by "manually," but I suspect that is the way it has to be done, at least if you want to control exactly which residues are used.  Basically as you described,

(1) somehow select the residues you want to use for superposition; sounds like you would select the two largest ligands, then do a zone selection around that initial selection (e.g. menu: Select... Zone), then maybe write out the list of selected residues (menu: Actions... Write List, choose "residues") to either Reply Log or file

(2) use the "match" command specifying the amino acid residues in that list (omitting other stuff like ligands and water) as the atoms to fit. This fit is pairwise, so you would need to decide which model you want as the reference and then use a separate match command to superimpose each of the remaining models onto it. There must be equal numbers of atoms specified for the two models, but they don't need to have the same residue numbering as each other. The tedious part is listing all the atoms (residues) in the command. 

** The much less tedious way is to use Matchmaker (or its command version) instead of the "match" command, as that will automatically figure out which set of residues to use and how they pair up. Personally, I would try Matchmaker first, because with default settings it generally does a very good job of superimposing the conserved core.  It automatically discards the poorly superimposed parts from the fit.

Superposition methods are discussed here:

Match command examples:
match #1:12,15,29-33 #0:12,15,29-33
... to use all atoms of the residues
match #2:15-18,85 at n,ca,c,o #0:26-29,116 at n,ca,c,o
... to use backbone atoms of the residues
See command-line atom specification:

You can sometimes decrease the tedium of retyping long specifications using "alias" to assign a shorter alias to the long string.  You still have to type it once in the "alias" command.  If it's really long, I'd probably use a text-editor to create a command file with the aliases in it.  Example with alias (and you could use 2 different aliases if the two structures have different numbering):
alias list1 :12,15,29-33 at ca
match #1 & list1 #0 & list1


Or you could just use a text-editor to create a command file with the match commands in it. Any method where you specify the exact atoms will be tedious if the list of atoms is long, sorry. I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 28, 2013, at 12:09 PM, Markus Heller wrote:

> Hello all,
> I’m pretty sure this has been done before, so before re-inventing the wheel or failing miserably and doing everything by hand, I thought I’d ask here first J
> I have a protein that has been crystallized with about a dozen ligands of different sizes.  I’d like to overlap the protein residues forming the binding site.  My plan was to pick the 2 largest ligands, select all protein residues within say 7 A, and consider these to be the residues forming the binding site.
> Then, I’d like to match this set of residues for all proteins to the same reference.
> I suppose I could do this all manually, but I’m hoping that there is a quicker, more efficient way! 
> Any tips are appreciated! 
> Thanks and Cheers
> Markus

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