[Chimera-users] Ligand Center of Mass

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 10 10:18:22 PDT 2017


Dear Armin,
There are actually two different commands you could use:

“define centroid” has option to do mass-weighting or not (treating each atom equally) and shows the result with a small sphere
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#centroid>

“measure center” does mass-weighting only and creating a marker (fake atom) at the position is optional
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center>

The result is reported in the Reply Log (open from Favorites menu).

They give the same numerical results, so you could use either one, but each has advantages if you want to do other things afterward.  For example, if you want to display a dashed-line distance measurement to the centroid, use “measure" since you need a fake atom for that.  If you want to define other geometric objects like ring planes or helix axes and make measurements among them (along with the centroid), then “define” is nicer for showing all those things in a graphical interface. Also, you can use the graphical tool instead of the command to define the centroid and other objects:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>

The structure 1G6N has two copies of the protein and two molecules of cAMP, so assuming you want the COM of only one molecule, you have to specify which one, unless you already deleted the other copy.  If I put the mouse over the ligand I can see its residue name is CMP and that the two chains (copies) are A and B.

In your case:
open 1g6n
focus :cmp.a
define centroid mass true radius 0.25 color magenta :cmp.a 
measure center :cmp.a mark true radius 0.3 color yellow

Reply Log shows:
centroid name, ID, center: centroid: c1 ( 38.831,  44.523,  49.339)
Center of mass of 22 atoms in 1g6n (#0) coordinate system = (38.83, 44.52, 49.34)

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

P.S. if you search for “center of mass” from the Chimera website (top right):
<http://www.rbvi.ucsf.edu/chimera/index.html>
or menu: Help… Search Documentation
…it would help you find these commands/tools

> On Jul 10, 2017, at 6:16 AM, ARMIN HODAEI <ahodaei15 at ku.edu.tr> wrote:
> 
> Dear Chimera users,
>       I have been wondering, is there a way to find a ligand Mass weighted center of mass in Chimera? 
> For example in the 1G6N(rcsb ID) protein I want to know the cAMP ligand's COM.
> Best,
> -- 
> Armin Hodaei
> Department of Physics,
> Faculty of Arts and Sciences
> Koc University, Istanbul
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