Hi Khawar,

  In a print journal your image might be half a page wide, about 4 inches, or a full page wide, about 8 inches.  To make the images 600 dots per inch you want those 2400 pixels wide or 4800 pixels wide.  To get that in ChimeraX you just specify the width

save myimage.png width 2400

The height will be chosen to match the shape of the ChimeraX graphics shown on the screen.

Tom


On Sep 8, 2025, at 7:35 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

Just to add to Ricardo's answer: with ChimeraX you can choose the width and height of your image in pixels, then when you insert it into your vector file you can choose the physical size it will have. I don't know about other programs, but at least Inkscape will let you choose any unit to express this size in, including inches.

So, to make sure you comply with the journal's requirements, insert your image in your vector file, resize it and place it where you want it in your final layout, then check its size in inches. Divide the size in pixels you generated from ChimeraX by the size in inches it will end up being scaled to in your figure: you get some number in ppi (pixels per inch, also called dpi for dots per inch). If this number is larger than what the journal wants, you're good to go. If it is smaller, generate the image from ChimeraX again, at a larger size in pixels (or conversely resize it to a smaller size in inches in your figure, but typically you want a specific size in the figure so it makes more sense to increase the size in pixels when saving from ChimeraX than to decrease the size in inches in your figure).

I hope this helps,

Guillaume
From: Ricardo Righetto via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Sent: Monday, September 8, 2025 4:00:31 PM
To: Khawar Siddiqui
Cc: Tom Goddard via ChimeraX-users
Subject: [chimerax-users] Re: High-Resolution images
 
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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