Small correction, the first link should be: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html> ...or you can use ChimeraX command "help define" to show the same help page included with your download.
On Mar 28, 2023, at 8:31 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Leo, Your chimeraX image with yellow dashed line is showing the closest distance to the plane, which is not necessarily the center of the ring. To show a dashed line to the center of the ring you would need to calculate a centroid of the ring (instead of the plane of the ring) and then measure distance between the centroid and the atom.
E.g. if you select the 6 ring atoms (Ctrl-click first atom, Shift-Ctrl-click each of the other 5) then you could use the Axes/Planes/Centroids tool or the "define" command to define their centroid, for example:
define centroid sel radius 0.25
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.htm> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/axesplanes.html>
Then you can measure distance between the centroid and the atom, e.g. Ctrl-click the centroid, Ctrl-Shift-doubleclick the atom and choose Distance from the resulting pop-up menu.
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 28, 2023, at 3:52 AM, 12119007 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello chimerax developers pannel, Bother to ask, I'm using chimerax to show an arginine forming a Π-cation bond with a phenyl ring， I don't know how to show the center of the phenyl ring like in pymol. I'm writing the order like this: distance /A:103@NH2 #1.4 and #1.4 is a plane I defined the phenyl ring. but it just show the distance but can't show the dash. Please tell me how to do. Any help I'm really appreciate. Thanks. <BE054F93-9BD3-4FDC-9E49-660D67BD8069.png><E2104D7E-B06A-41FA-A3B2-3CAFE1FFD3D5.png> Leo
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users