Hi Ramy, I tried to change the subject line to a useful description so that others would be able to find it later in our archive. If you mean one specific molecule, you could save a session file. Every time you restore the session it will have the coloring etc. from when you saved it. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session> If you mean it is a color scheme you might want to apply to various different structures when you open them, you may want to define a custom preset as explained here: <http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup> Basically you would put the commands in a file and then use the Startup section of the Preferences to specify it as a custom preset. Details in the link above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Oct 20, 2020, at 5:26 AM, Kazan Ramy (M.) <ramy.kazan@polytechnique.edu> wrote:

Greetings to all,

When opening a new molecule, ChimeraX automatically apply a color to my molecule. I know how to modify the colors, which is very fun especailly using the command line but also very time consuming for multi-chain molecules.

I would like to impose a coloring scheme for a model by default, that way everytime I open the model the coloring is the same for the my molecule.

I guess one way is to use the function key but this would be limited to a mixumum of twelve molecules and is atom-spec dependent so not very practical.

Is there a way to permently save the information, maybe in the pdb file header/footer, or somewhere else?

Ramy Kazan PhD Student