[chimerax-users] Placing Centroid at center of selection

[Elaine Meng]

Hi German, 
Sure!  "sel" is an atom specification that means the currently selected atoms.  So if you have selected the atoms of the benzene ring, it would be something like:

define centroid sel radius 0.25 color orange

...where "sel" is the atom-spec as shown in the usage information:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#centroid>

There are lots of different ways to give an atom-spec.  Instead of "sel" you could give residue number(s) or name(s), atom name(s), "protein" etc.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

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

> On Mar 16, 2022, at 4:45 PM, German Barcenas via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> I am trying to place a centroid marker at the center of a selection of atoms, for example in the middle of a benzene ring that is at some arbitrary position in my system. I want to do some distance measurements here. I can do something like this:
> 
> shape sphere color orange radius 0.25 center sel
> 
> where the center sel places the sphere where I want, but these spheres can't be used to make measurements. Instead I think I need a marker object, such as:
> 
> define centroid radius 0.25 color orange 
> 
> But I don't know how to recreate that `center sel` position. I have tried 
> 
> define centroid radius 0.25 color orange position center
>  
> define centroid radius 0.25 color orange position center sel
> 
> define centroid radius 0.25 color orange position sel
> 
> These do not work. I am under the impression that the centroid is a marker object and should have some position argument. Can anyone help me?
> Thanks,