Question about density map visualization for figures using ChimeraX
Hello, I am currently preparing figures for a publication and am using ChimeraX to render a density map. The color of the mesh representation I am using is set to *licorice*, but after I save the image in TIFF/PNG format at 7602 × 5680 resolution, the mesh appears quite faint. Could you please advise on how to make the density appear darker or more prominent in the saved image? Thank you! -Abhipsa
Hello, ChimeraX does not have any option to thicken the mesh lines, so when you save an image at high resolution they turn out very thin. For an explanation of why there isn't an option, see <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2018-September/000315.htm...> There isn't a color named licorice, but this issue is the same regardless of what the color is. Our older program Chimera had a "meshmol" command to create a fake molecule so that the mesh could be shown as stick "bonds," but as far as I know ChimeraX does not have that. Some people have tried selecting the mesh (and you could change selection color to black instead of lime, see command "graphics selection"), but it does not look good in saved images. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#selection> Sorry about this limitation, 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 Oct 22, 2025, at 3:20 PM, Abhipsa Shatarupa via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am currently preparing figures for a publication and am using ChimeraX to render a density map. The color of the mesh representation I am using is set to licorice, but after I save the image in TIFF/PNG format at 7602 × 5680 resolution, the mesh appears quite faint. Could you please advise on how to make the density appear darker or more prominent in the saved image? Thank you! -Abhipsa _______________________________________________ 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 Abhipsa, ChimeraX uses modern OpenGL graphics (core profile) which only supports 1 pixel wide lines. So when you make a 7600 pixel wide image those are pretty thin. The easy solution is to not make a 7600 pixel wide image, and instead use say 1000 pixels wide. If you are going for 300 pixels per inch the 7600 pixel image is more than 2 feet wide. But if you really do need a 2 foot wide image at print resolution you could convert the mesh to a marker model which makes each line a cylinder. It can take a long time for a large mesh, but is fine for a small mesh. Here's an example marker fromMesh #1.1 edgeRadius 0.05 Documentation here https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html Tom Example marker mesh will retain its line thickness in Angstroms since each line is drawn as a thin cylinder. 
On Oct 22, 2025, at 3:20 PM, Abhipsa Shatarupa via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am currently preparing figures for a publication and am using ChimeraX to render a density map. The color of the mesh representation I am using is set to licorice, but after I save the image in TIFF/PNG format at 7602 × 5680 resolution, the mesh appears quite faint.
Could you please advise on how to make the density appear darker or more prominent in the saved image?
Thank you!
-Abhipsa
_______________________________________________ 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/
ChimeraX shows electron density mesh as a line object and you can’t adjust the width. A hack around this is to select the map and color the selection to match. For example if your map is #2: select #2 graphics selection color licorice color #2 licorice -- Kevin M. Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 From: Abhipsa Shatarupa via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: Wednesday, October 22, 2025 at 3:22 PM To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Question about density map visualization for figures using ChimeraX Hello, I am currently preparing figures for a publication and am using ChimeraX to render a density map. The color of the mesh representation I am using is set to licorice, but after I save the image in TIFF/PNG format at 7602 × 5680 resolution, the mesh appears quite faint. Could you please advise on how to make the density appear darker or more prominent in the saved image? Thank you! -Abhipsa
participants (4)
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Abhipsa Shatarupa -
Elaine Meng -
Kevin M Jude -
Tom Goddard