Request to Resolve the Issue of Modifying Surface Dot Size in ChimeraX
Dear ChimeraX Maintenance Team,
I hope this email finds you well. I am writing to seek assistance regarding an issue I have encountered while working with protein models in ChimeraX.
After performing MPL calculations on protein models, I have found that I am unable to modify the dot size of the resulting surface representation. In Chimera, this task was easily accomplished through the "Model Panel" by adjusting the "MSMS Model Attributes". However, I have not been able to find a similar option or command in ChimeraX.
I would greatly appreciate it if you could provide guidance or suggest a solution to address this matter. Being able to adjust the dot size of the surface representation is crucial for my current research project, and I rely heavily on the functionalities provided by ChimeraX.
Thank you very much for your attention to this matter. I look forward to your kind assistance and prompt response.
Best regards, Zhuangwei Zhang, Ph.D. State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Centre of Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University E-mail: dg21240166@smail.nju.edu.cn
Dear Zhuangwei Zhang, Sorry, ChimeraX does not have any way to increase dot size (or line width).
As I understand it, this is due to changes in OpenGL. There is an explanation for line width in this previous post, and as far as I know the explanation for dot size is the same:
Instead of showing the surface as dots, maybe you could show it as mesh (although linewidth cannot be increased) or solid using a transparent color.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#style
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 14, 2023, at 3:50 AM, 18802001045--- via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX Maintenance Team,
I hope this email finds you well. I am writing to seek assistance regarding an issue I have encountered while working with protein models in ChimeraX.
After performing MPL calculations on protein models, I have found that I am unable to modify the dot size of the resulting surface representation. In Chimera, this task was easily accomplished through the "Model Panel" by adjusting the "MSMS Model Attributes". However, I have not been able to find a similar option or command in ChimeraX.
I would greatly appreciate it if you could provide guidance or suggest a solution to address this matter. Being able to adjust the dot size of the surface representation is crucial for my current research project, and I rely heavily on the functionalities provided by ChimeraX.
Thank you very much for your attention to this matter. I look forward to your kind assistance and prompt response.
Best regards, Zhuangwei Zhang, Ph.D. State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Centre of Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University E-mail: dg21240166@smail.nju.edu.cn
One workaround that sometimes works to make it look like the mesh has thicker lines is to use the silhouette settings to make the silhouette lines of the correct color (matching the mesh) and of desired width: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouett...
But you cannot have silhouettes drawn around some objects and not others (AFAIK), so this is not a general solution.
Cheers, Alexis
On Thu, Sep 14, 2023 at 9:02 AM Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Zhuangwei Zhang, Sorry, ChimeraX does not have any way to increase dot size (or line width).
As I understand it, this is due to changes in OpenGL. There is an explanation for line width in this previous post, and as far as I know the explanation for dot size is the same:
< https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...
Instead of showing the surface as dots, maybe you could show it as mesh (although linewidth cannot be increased) or solid using a transparent color.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#style
Regards, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 14, 2023, at 3:50 AM, 18802001045--- via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Maintenance Team,
I hope this email finds you well. I am writing to seek assistance
regarding an issue I have encountered while working with protein models in ChimeraX.
After performing MPL calculations on protein models, I have found that I
am unable to modify the dot size of the resulting surface representation. In Chimera, this task was easily accomplished through the "Model Panel" by adjusting the "MSMS Model Attributes". However, I have not been able to find a similar option or command in ChimeraX.
I would greatly appreciate it if you could provide guidance or suggest a
solution to address this matter. Being able to adjust the dot size of the surface representation is crucial for my current research project, and I rely heavily on the functionalities provided by ChimeraX.
Thank you very much for your attention to this matter. I look forward to
your kind assistance and prompt response.
Best regards, Zhuangwei Zhang, Ph.D. State Key Laboratory of Analytical Chemistry for Life Science,
Collaborative Innovation Centre of Chemistry for Life Sciences
School of Chemistry and Chemical Engineering Nanjing University E-mail: dg21240166@smail.nju.edu.cn
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/
Yes unfortunately the maximum point size is driver dependent and the only required size is 1, but you can query (glGetIntegerv) GL_POINT_SIZE_RANGE. I was unhappy with the single pixel size on HiDPI displays for my segmentation tool, so code in https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/dicom/src/graphics... attempts to set it to something a little thicker if the driver allows (looking at this code again I can see how I could do it once and not every draw call).
Hope this helps,
— Zach
On Sep 14, 2023, at 09:55, Alexis Rohou via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
One workaround that sometimes works to make it look like the mesh has thicker lines is to use the silhouette settings to make the silhouette lines of the correct color (matching the mesh) and of desired width: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouett...
But you cannot have silhouettes drawn around some objects and not others (AFAIK), so this is not a general solution.
Cheers, Alexis
On Thu, Sep 14, 2023 at 9:02 AM Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Dear Zhuangwei Zhang, Sorry, ChimeraX does not have any way to increase dot size (or line width).
As I understand it, this is due to changes in OpenGL. There is an explanation for line width in this previous post, and as far as I know the explanation for dot size is the same:
Instead of showing the surface as dots, maybe you could show it as mesh (although linewidth cannot be increased) or solid using a transparent color.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#style
Regards, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 14, 2023, at 3:50 AM, 18802001045--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Maintenance Team,
I hope this email finds you well. I am writing to seek assistance regarding an issue I have encountered while working with protein models in ChimeraX.
After performing MPL calculations on protein models, I have found that I am unable to modify the dot size of the resulting surface representation. In Chimera, this task was easily accomplished through the "Model Panel" by adjusting the "MSMS Model Attributes". However, I have not been able to find a similar option or command in ChimeraX.
I would greatly appreciate it if you could provide guidance or suggest a solution to address this matter. Being able to adjust the dot size of the surface representation is crucial for my current research project, and I rely heavily on the functionalities provided by ChimeraX.
Thank you very much for your attention to this matter. I look forward to your kind assistance and prompt response.
Best regards, Zhuangwei Zhang, Ph.D. State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Centre of Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University E-mail: dg21240166@smail.nju.edu.cn mailto:dg21240166@smail.nju.edu.cn
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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 Elaine, Zhuangwei,
Although the OpenGL standard deprecated line widths other than 1 pixel, surprisingly it still supports point sizes greater than 1 pixel. But ChimeraX does not have support for points larger than 1 pixel currently. Point drawings are rare so this has not been a priority. I've made a ChimeraX feature request to allow surfaces to specify the size of the points when shown in dot style.
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9785
Adding a line of code to ChimeraX Python like Zach suggested can allow you to show larger points. You would edit this Python file in a text editor
ChimeraX.app/Contents/lib/python3.11/site-packages/chimerax/graphics/opengl.py
(this is the location on Mac, different on Windows and Linux) and you after the these lines in the make_current() function
if not qc.makeCurrent(w): raise OpenGLError("Could not make graphics context current")
you would add a call to glPointSize()
if not qc.makeCurrent(w): raise OpenGLError("Could not make graphics context current")
GL.glPointSize(8)
and that will make your points 8 pixel wide squares. I include an image of a dot surface below showing what those ugly large square points look like for a molecular surface. There is no easy way to make the points circles -- that requires graphics shader code in modern OpenGL.
Tom
ChimeraX points of size 8. 
On Sep 14, 2023, at 9:01 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Zhuangwei Zhang, Sorry, ChimeraX does not have any way to increase dot size (or line width).
As I understand it, this is due to changes in OpenGL. There is an explanation for line width in this previous post, and as far as I know the explanation for dot size is the same:
Instead of showing the surface as dots, maybe you could show it as mesh (although linewidth cannot be increased) or solid using a transparent color.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#style
Regards, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 14, 2023, at 3:50 AM, 18802001045--- via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX Maintenance Team,
I hope this email finds you well. I am writing to seek assistance regarding an issue I have encountered while working with protein models in ChimeraX.
After performing MPL calculations on protein models, I have found that I am unable to modify the dot size of the resulting surface representation. In Chimera, this task was easily accomplished through the "Model Panel" by adjusting the "MSMS Model Attributes". However, I have not been able to find a similar option or command in ChimeraX.
I would greatly appreciate it if you could provide guidance or suggest a solution to address this matter. Being able to adjust the dot size of the surface representation is crucial for my current research project, and I rely heavily on the functionalities provided by ChimeraX.
Thank you very much for your attention to this matter. I look forward to your kind assistance and prompt response.
Best regards, Zhuangwei Zhang, Ph.D. State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Centre of Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University E-mail: dg21240166@smail.nju.edu.cn
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/
participants (5)
-
18802001045＠163.com -
Alexis Rohou -
Elaine Meng -
Tom Goddard -
Zach Pearson