[Chimera-users] Ligand Center of Mass

[ARMIN HODAEI]

Dear Elaine,


     It was very helpful. Thank you very much for your kind attention.

Armin


On Mon, Jul 10, 2017 at 8:18 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
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>
>


-- 
Armin Hodaei
Department of Physics,
Faculty of Arts and Sciences
Koc University, Istanbul
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