Hi Natalia - try changing the file format you are saving as to 'ChimeraX Session' (.cxs) - this will capture the colours, how the molecules are rotated and shown and lots more.

Hope that helps !

Jim

From: Natalia Tegenfeldt via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Sent: 25 August 2023 15:23
To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] Changing Colors and Unable to Save as pdb File

I have been using chimerax to visualize the proteins I'm working with, and have been highlighting sections of the sequence and changing the color to highlight those sections, but when I try to save it as a pdb, it gets rid of the colors. Is there a different way to be able to keep a section highlighted/different color when I save it as a pdb file?

Thanks!

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