Hi Elaine, Thank you for the suggestions. I will experiment with the granular coloring options you gave to see if I can get the look I'm going for. All the best, Joel On 4/7/20, 1:36 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: Hi Joel, ChimeraX currently does not have a "highlight color" (an option to use a different color for the inside of helices). However, otherwise you can color helix/strand/other any colors you like. You just specify "helix" or "strand" in the "color" command, using the "target" option of the command to limit the coloring to only the cartoons (target c) and/or atoms, surface patches, etc. <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... > <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... > For example, color protein gold target c color helix hot pink targ c color strand #48d1cc targ c For the colors themselves, there are many names built in, or you can use hex codes or R,G,B, etc. You can see the names + color swatches listed alphabetically in the Log with command "color list" but they are more organized by color in the table here: <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... > If you like to use a certain trio of colors repeatedly you can put the three commands into a .cxc file and define them as a custom preset, to be listed in your Presets menu for easy use. See Preferences, category:Startup to define a custom preset. <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... > I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 7, 2020, at 10:01 AM, Joel Meyerson <jrm2008@med.cornell.edu> wrote: > > Hi, > Is there a way to customize the highlight color of helices and strands? For example, here is how it appears in Pymol. > > https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php... > > Thanks, > Joel