Question in using ChimeraX ----mesh parameters
Hello developers, I have a question in using ChimeraX. May I ask how can I change the density of grids and line size of the mesh for a volume? Best, Shuhui
Hi Shuhui, There is no option to change the mesh line width in ChimeraX, sorry. The grid density displayed when you first open the map depends on the data, i.e. if your map file grid has values 1 angstrom apart that is what the mesh will show (if you are also at step 1). You can change the step size in the Volume Viewer tool or with the "volume" command "step" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling> However, the "volume" command has options "subdivideSurface" and "subdivisionLevels" to draw more triangles in the mesh, as well as "squareMesh" to draw fewer lines: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf> For example, command: volume #2 subdivide true subdivisionLevels 1 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 24, 2023, at 6:05 AM, Wang, Shuhui via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello developers,
I have a question in using ChimeraX. May I ask how can I change the density of grids and line size of the mesh for a volume?
Best, Shuhui
Hi Elaine, I got. Thank you so much. Best, Shuhui ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, March 24, 2023 12:30 PM To: Wang, Shuhui <Shuhui_Wang@hms.harvard.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Question in using ChimeraX ----mesh parameters Hi Shuhui, There is no option to change the mesh line width in ChimeraX, sorry. The grid density displayed when you first open the map depends on the data, i.e. if your map file grid has values 1 angstrom apart that is what the mesh will show (if you are also at step 1). You can change the step size in the Volume Viewer tool or with the "volume" command "step" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling> However, the "volume" command has options "subdivideSurface" and "subdivisionLevels" to draw more triangles in the mesh, as well as "squareMesh" to draw fewer lines: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf> For example, command: volume #2 subdivide true subdivisionLevels 1 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 24, 2023, at 6:05 AM, Wang, Shuhui via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello developers,
I have a question in using ChimeraX. May I ask how can I change the density of grids and line size of the mesh for a volume?
Best, Shuhui
HI Shuhui, Unfortunately the OpenGL 3D graphics standard which ChimeraX uses dropped support for rendering lines thick than 1 pixel many years ago. The 1 pixel thick lines are very thin on 4K and retina displays so we would like thicker lines so meshes are more visible. The OpenGL standard "deprecated" lines greater than 1 pixel wide, but I tested to see if current graphics drivers still support thicker lines. I found that Mac OpenGL only supports 1 pixel wide lines. But on Windows and Linux if I request support for deprecated functions then Nvidia drivers still provide lines up to 10 pixels wide. That support may be removed from the drivers in the future. I have not enabled it in ChimeraX, although I may in the future ask 4K displays become more common on Linux and Windows. Unfortunately the high resolution displays are most common on Mac which does not offer the wider lines. These limitations are recorded in this ChimeraX issue https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/1315 and if I add support for the deprecated thicker lines on Windows and Linux it will be noted there. Tom
On Mar 24, 2023, at 9:30 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Shuhui,
There is no option to change the mesh line width in ChimeraX, sorry.
The grid density displayed when you first open the map depends on the data, i.e. if your map file grid has values 1 angstrom apart that is what the mesh will show (if you are also at step 1). You can change the step size in the Volume Viewer tool or with the "volume" command "step" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling>
However, the "volume" command has options "subdivideSurface" and "subdivisionLevels" to draw more triangles in the mesh, as well as "squareMesh" to draw fewer lines: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf>
For example, command:
volume #2 subdivide true subdivisionLevels 1
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 24, 2023, at 6:05 AM, Wang, Shuhui via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello developers,
I have a question in using ChimeraX. May I ask how can I change the density of grids and line size of the mesh for a volume?
Best, Shuhui
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participants (3)
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Elaine Meng -
Tom Goddard -
Wang, Shuhui