Page Title

I think what throws you off is the aspect ratio of the ChimeraX window. Add a command to set the size of the window into your workflow. For example:

windowsize 800 800

Regards,

Daniel

From: Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Reply to: Samuel Haysom <Samuel.Haysom@Nxera.life>
Date: Monday, 9 June 2025 at 17:10
To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] Robust way to setup scene and save image such that zoom and resolution are always the same across different monitors

Hello,

Is there a recommended set of commands to setup a particular view of a molecule and then save an image of that view such that the size of the molecule within the image, the resolution of the image, and the position of the clipping planes will always be the same regardless of what monitor size/resolution it is taken on?

Currently I setup an image using the following commands:

e.g.

view matrix camera 0.98237,-0.066404,-0.17474,86.421,0.014131,-0.90572,0.42363,190.37,-0.1864,-0.41863,-0.88882,-48.082

clip near -10 far 10 position /R:LIG

zoom pixel 0.0348

I then save it using:

e.g.

save 'dir_path/image.png' width 2000 height 2000 supersample 10 transparentBackground False

I often will come back to the same cxc script and want to re-render with e.g. a modified pdb file but still want to get exactly the same view. I can then substitute this picture into a figure I've created in e.g. Inkscape without having to resize the image. However I've noticed that often the new image will not have the same zoom (so the model will be bigger and smaller within the total FOV) which means I have to then manually resize it to match what I already have. I've also noticed that if I render on e.g. my laptop rather than my desktop monitors this effects both the zoom as previously mentioned but also the final resolution of the image as this seems tied to the screen resolution.

Is there a way to make it so the image will always look the same regardless of hardware etc.?

KR,

Sam

Samuel Haysom

Senior Scientist

•

Protein Sciences

Nxera Pharma UK Limited

+44 (0)1223 949201

•

Steinmetz Building, Granta Park, Great Abington
Cambridge, CB21 6DG, United Kingdom

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