On Mar 29, 2023, at 6:19 AM, 12119007 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello Elaine,

Thank you so mach for your kindly help. I have succeeded in defining the centroids, but when I click the distance between centroids to the atom I chosed, it report this bug. I don't know if there's some thing I did wrong. Let me know if something I can do.Thank you so much.

                                                   Leo     

  

<E473B256-5FCC-4823-AEEB-13A542E873EA.png> 

<A52D4FCF-E872-44AE-A88F-BD86DC514908.png>

	12119007
12119007@zju.edu.cn

---- Replied Message ----

From	Elaine Meng<meng@cgl.ucsf.edu>
Date	3/28/2023 23:45
To	12119007<12119007@zju.edu.cn>
Cc	Elaine Meng via ChimeraX-users<chimerax-users@cgl.ucsf.edu>
Subject	Re: [chimerax-users] measure distance to ring centroid

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

_______________________________________________
ChimeraX-users mailing list
ChimeraX-users@cgl.ucsf.edu
Manage subscription:
https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users