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<div>Hello Elaine,</div><div style="text-indent: 2em;">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.</div><div style="text-indent: 2em;"> Leo </div><div style="text-indent: 2em;"> </div>
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<a class="mail-from" style="color: #3061f2; text-decoration: none" href="mailto:meng@cgl.ucsf.edu">Elaine Meng<meng@cgl.ucsf.edu>
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3/28/2023 23:45
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12119007<12119007@zju.edu.cn>
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Elaine Meng via ChimeraX-users<chimerax-users@cgl.ucsf.edu>
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Re: [chimerax-users] measure distance to ring centroid
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<div id="ntes-pcmail-quote" style="margin: 0; padding: 0; font-size: 14px; font-family: '微软雅黑';">Small correction, the first link should be:<br><br><https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html><br><br>...or you can use ChimeraX command "help define" to show the same help page included with your download.<br><br> <blockquote class="mmbqc1">On Mar 28, 2023, at 8:31 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br> <br> Hi Leo,<br> 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.<br> <br> 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:<br> <br> define centroid sel radius 0.25<br> <br> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.htm><br> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/axesplanes.html><br> <br> 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.<br> <br> I hope this helps,<br> Elaine<br> -----<br> Elaine C. Meng, Ph.D. <br> UCSF Chimera(X) team<br> Department of Pharmaceutical Chemistry<br> University of California, San Francisco<br> <br> <br> <blockquote class="mmbqc2">On Mar 28, 2023, at 3:52 AM, 12119007 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br> <br> Hello chimerax developers pannel, <br> 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.<br> <BE054F93-9BD3-4FDC-9E49-660D67BD8069.png><E2104D7E-B06A-41FA-A3B2-3CAFE1FFD3D5.png> Leo<br> </blockquote><br> <br> _______________________________________________<br> ChimeraX-users mailing list<br> ChimeraX-users@cgl.ucsf.edu<br> Manage subscription:<br> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br> <br></blockquote></div>
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