Hi, I'm a researcher from India. I have been trying to make some EM fitting image with model protein. There is no Volume viewer option for Line smoothening, surface smoothening or square mesh to triangle mesh conversion. Also surface smoothening problem. I have been trying to execute through the command line, but it doesnt work . Can you help me regarding command line code for following Mesh Line smoothing Mesh surface smoothening Dim transparency The suite is ChimeraX or ChimeraX 1.9 Regards, Akash Singh
Hello Akash, Yes, this is all in the "volume" command options. The "usage" in the help page shows how to use the command, e.g. see the section on mesh display options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf> Example command, if your map is model #2 ... volume #2 surfaceSmoothing true smoothLines true meshLighting true See the link above for more options, like how many smoothing iterations, etc. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 23, 2025, at 4:27 AM, Akash Singh via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I'm a researcher from India. I have been trying to make some EM fitting image with model protein. There is no Volume viewer option for Line smoothening, surface smoothening or square mesh to triangle mesh conversion. Also surface smoothening problem. I have been trying to execute through the command line, but it doesnt work . Can you help me regarding command line code for following Mesh Line smoothing Mesh surface smoothening Dim transparency
The suite is ChimeraX or ChimeraX 1.9
Regards, Akash Singh
Hi Akash, Elaine, The ChimeraX volume command "smoothLines" option is not implemented. It should probably be removed from the documentation and the command. The reason it is not implemented is that the OpenGL graphics GL_LINE_SMOOTH capability was removed in modern OpenGL. The modern way to get a smoother appearance is multisampling which smooths the entire scene. ChimeraX has not implemented multisampling on screen, but the supersample option when saving an image does it. The other volume options Elaine mentioned are supported in ChimeraX. Tom
On Jun 23, 2025, at 1:45 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Akash, Yes, this is all in the "volume" command options. The "usage" in the help page shows how to use the command, e.g. see the section on mesh display options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf>
Example command, if your map is model #2 ...
volume #2 surfaceSmoothing true smoothLines true meshLighting true
See the link above for more options, like how many smoothing iterations, etc.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 23, 2025, at 4:27 AM, Akash Singh via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I'm a researcher from India. I have been trying to make some EM fitting image with model protein. There is no Volume viewer option for Line smoothening, surface smoothening or square mesh to triangle mesh conversion. Also surface smoothening problem. I have been trying to execute through the command line, but it doesnt work . Can you help me regarding command line code for following Mesh Line smoothing Mesh surface smoothening Dim transparency
The suite is ChimeraX or ChimeraX 1.9
Regards, Akash Singh
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hello ElaineCan I set the mailing to receive just my emails? Can you tell me how to do this setting?Thanks you very much!Mariela On Monday, June 23, 2025 at 02:48:07 PM GMT-3, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hello Akash, Yes, this is all in the "volume" command options. The "usage" in the help page shows how to use the command, e.g. see the section on mesh display options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf> Example command, if your map is model #2 ... volume #2 surfaceSmoothing true smoothLines true meshLighting true See the link above for more options, like how many smoothing iterations, etc. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 23, 2025, at 4:27 AM, Akash Singh via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I'm a researcher from India. I have been trying to make some EM fitting image with model protein. There is no Volume viewer option for Line smoothening, surface smoothening or square mesh to triangle mesh conversion. Also surface smoothening problem. I have been trying to execute through the command line, but it doesnt work . Can you help me regarding command line code for following Mesh Line smoothing Mesh surface smoothening Dim transparency
The suite is ChimeraX or ChimeraX 1.9
Regards, Akash Singh
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Mariela, I changed the subject line. I am not sure what you are asking. The only choices are to receive all chimerax-users emails (if you subscribe to the list) or none of them (unsubscribe). To unsubscribe you would follow the instructions at the bottom of the message:
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Usually if you ask a question to chimerax-users, however, the person who answers will often include your individual email address in the reply (in addition to chimerax-users) and then you would receive the reply even if you are unsubscribed from chimerax-users emails. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 26, 2025, at 4:09 AM, mariela Urrutia via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Elaine Can I set the mailing to receive just my emails? Can you tell me how to do this setting? Thanks you very much! Mariela
Thank you so much for the info. It works after reinstalling chimera. It took me time to figure it out, so I delayed in reply. Thank you! Regards, Akash Singh On Mon, Jun 23, 2025 at 11:15 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Akash, Yes, this is all in the "volume" command options. The "usage" in the help page shows how to use the command, e.g. see the section on mesh display options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf>
Example command, if your map is model #2 ...
volume #2 surfaceSmoothing true smoothLines true meshLighting true
See the link above for more options, like how many smoothing iterations, etc.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 23, 2025, at 4:27 AM, Akash Singh via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi, I'm a researcher from India. I have been trying to make some EM fitting image with model protein. There is no Volume viewer option for Line smoothening, surface smoothening or square mesh to triangle mesh conversion. Also surface smoothening problem. I have been trying to execute through the command line, but it doesnt work . Can you help me regarding command line code for following Mesh Line smoothing Mesh surface smoothening Dim transparency
The suite is ChimeraX or ChimeraX 1.9
Regards, Akash Singh
participants (4)
-
Akash Singh -
Elaine Meng -
mariela Urrutia -
Tom Goddard