Hi Natalia, Jim's answer is the best, since ChimeraX session is probably what you want.

Here are some more thoughts and details if you are interested...

PDB files do not contain colors. PDB files contain the atomic coordinates, bonds, and secondary structure, but not details of how the structure is displayed.

If you want to save colors, it depends what program you want to open the saved file in. You can save an image file, or you can save a ChimeraX session if you are going to reopen it in ChimeraX. Some other save formats also include color, but again, it depends in which program you plan to open the file, since that program may not be able to read that kind of file.

Saving image files https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image https://rbvi.ucsf.edu/chimerax/docs/user/images.html

Saving ChimeraX sessions https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session

Exporting to GLTF or OBJ https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Aug 25, 2023, at 7:43 AM, James Procter (Staff) via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

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!