[chimerax-users] measure distance to ring centroid
Eric Pettersen
pett at cgl.ucsf.edu
Thu Mar 30 08:30:44 PDT 2023
Happy to help!
--Eric
> On Mar 30, 2023, at 5:57 AM, 12119007 via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> Hello Eric,
> Thank you so much for your help! It helps me a lot. I'm really appreciate that.
> Leo
>
>
> 12119007
>
> 12119007 at zju.edu.cn
> <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=12119007&uid=12119007%40zju.edu.cn&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fqiyelogo%2FdefaultAvatar.png&items=%5B%2212119007%40zju.edu.cn%22%5D&logoUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fqiyeicon%2Fdb5d090b4290fa1cc857f03f01662859.png>
> ---- Replied Message ----
> From Eric Pettersen<pett at cgl.ucsf.edu> <mailto:pett at cgl.ucsf.edu>
> Date 3/29/2023 23:54
> To 12119007<12119007 at zju.edu.cn> <mailto:12119007 at zju.edu.cn>
> Cc chimerax-users at cgl.ucsf.edu<chimerax-users at cgl.ucsf.edu> <mailto:chimerax-users at cgl.ucsf.edu>
> Subject Re: [chimerax-users] measure distance to ring centroid
> Hi Leo,
> Yes, that's a bug. The bug has been fixed, but the fix is only in the daily build and 1.6 release candidate builds, so you would have to install one of those to get this to work. Sorry about that.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
>> On Mar 29, 2023, at 6:19 AM, 12119007 via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at 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 at zju.edu.cn
>> <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=12119007&uid=12119007%40zju.edu.cn&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fqiyelogo%2FdefaultAvatar.png&items=%5B%2212119007%40zju.edu.cn%22%5D&logoUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fqiyeicon%2Fdb5d090b4290fa1cc857f03f01662859.png>
>> ---- Replied Message ----
>> From Elaine Meng<meng at cgl.ucsf.edu> <mailto:meng at cgl.ucsf.edu>
>> Date 3/28/2023 23:45
>> To 12119007<12119007 at zju.edu.cn> <mailto:12119007 at zju.edu.cn>
>> Cc Elaine Meng via ChimeraX-users<chimerax-users at cgl.ucsf.edu> <mailto:chimerax-users at 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 <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 at cgl.ucsf.edu <mailto:chimerax-users at 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/commands/define.htm>>
>> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/axesplanes.html <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 at cgl.ucsf.edu <mailto:chimerax-users at 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 at 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
>>
>>
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