Dear Elaine, Many thanks for the tip! saving as a *.cxs was exactly what I was missing. Cheers, Claudio On 23 Jul 2024, at 17:42, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Claudio, We're glad you like ChimeraX! PDB format does not include colors. It is only for the atomic coordinates. The usual way to save your work and come back to it later is to save and restore a ChimeraX session file (*.cxs). You can save that with the "save" command, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session> ... or you can save it with File... Save in the menu, if you choose the appropriate file type in the resulting dialog window. Then later you can start a new ChimeraX and restore your session from file by simply opening it (with File... Open in the menu, or with the "open" command). Of course you can save images and other formats too, but they would just be images etc. and not modifiable in ChimeraX. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 23, 2024, at 1:26 AM, Claudio Andres Aguilar Pena via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Dear ChimeraX team, First of all, many thanks for the app, it’s really wonderful!. I have a question regarding one feature I would like to have and maybe it’s possible to do but I just don’t know how. I have a PDB of the structure of an enzyme that has 5 different domains: I can select the aa of each domain and give each domain a color. This is very useful for me when comparing structure predictions of the enzyme and see what happens when making mutations in the primary structure. My problem is that I cannot save the PDB with the colors for each domain, so I have to select and assign the colors every time, or leave the app and the PDB permanently open, which is not very convenient. Is there a way to save the PDB with the modifications I made? Many thanks for your help. Best, Claudio Dr. Claudio Aguilar, PhD Virologisches Institut Universität Zürich Vetsuisse Fakultät Winterthurerstrasse 266a CH-8057 Zürich Switzerland phone: +41446358712 Fax: +41446358911