Ahh ok, so I was overcomplicating it I guess(: I just tried this and it worked. Thanks so much! On Wed, Mar 16, 2022 at 6:53 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
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@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,
-- German Barcenas Ph.D Candidate | Materials Science and Engineering Materials Modeling and Theory Group Boise State University germanbarcenas@u.boisestate.edu | 940-577-5094