question about chimerax
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
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
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@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 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 Mengmeng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu Date 3/28/2023 23:45 To 1211900712119007@zju.edu.cn mailto:12119007@zju.edu.cn Cc Elaine Meng via ChimeraX-userschimerax-users@cgl.ucsf.edu mailto: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 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 mailto: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/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@cgl.ucsf.edu mailto: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 mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Happy to help!
--Eric
On Mar 30, 2023, at 5:57 AM, 12119007 via ChimeraX-users chimerax-users@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@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 Pettersenpett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu Date 3/29/2023 23:54 To 1211900712119007@zju.edu.cn mailto:12119007@zju.edu.cn Cc chimerax-users@cgl.ucsf.educhimerax-users@cgl.ucsf.edu mailto:chimerax-users@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@cgl.ucsf.edu mailto: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 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 Mengmeng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu Date 3/28/2023 23:45 To 1211900712119007@zju.edu.cn mailto:12119007@zju.edu.cn Cc Elaine Meng via ChimeraX-userschimerax-users@cgl.ucsf.edu mailto: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 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 mailto: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/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@cgl.ucsf.edu mailto: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
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participants (3)
-
12119007 -
Elaine Meng -
Eric Pettersen