Re: [chimerax-users] Placing Centroid at center of selection

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 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,