Hi Khawar,

Typically, you will prepare figures for your manuscript using some vector image editing software (like Adobe Illustrator or Inkscape) and save them in a vector format like AI, SVG or PDF. Your figures may include multiple panels, arrows, shapes and raster images (PNG or TIFF). Normally, this is the file that the journal wants from you.
For the raster images that may go into your vector figure: if you use ChimeraX for, say, rendering a molecule, with the program's embedded command prompt you can export raster images with a command line like:

save my_figure.png transparentBackground true supersample 3 width 4096 height 2048

While you cannot adjust the dpi value directly, you can adjust the values of 'width' and 'height' to make arbitrarily high resolution (high dpi) files, more than enough for the journal.

Best wishes,

--
Ricardo Diogo Righetto


Em seg., 8 de set. de 2025 às 07:56, Khawar Siddiqui via ChimeraX-users <chimerax-users@cgl.ucsf.edu> escreveu:
Hi Tom,
Hope you are fine. Nature Computational Science requires high-resolution VECTOR images like PDF. I noticed that ChimeraX does not have this option. Secondly, I also noticed that images can not be exported with 300-600 dpi Raster files like TIFF or PNG.

How shall I proceed? I have no command-line experience.

Thanking you in advance.
Regards
Sohail

Dr Khawar Sohail Siddiqui,

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