Good morning Garrett, ChimeraX has a "color byattribute" command that is the logical equivalent of Chimera's "rangecolor." In ChimeraX, amino acid kdHydrophobicity is not assigned automatically, but you can assign it as a residue attribute and then use "color byattribute" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> ... in fact, I've already done the legwork for you on this one because it is our example of a custom preset, and you can certainly use the files I created, or create your own by analogy. This custom preset file (command script) is linked to the description of the ChimeraX preferences, Startup tab: <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup> <https://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle_hydrophobicity.cxc> However, you don't need to define a custom preset. You can just use the script that I provided directly, or the individual commands as you like. You can use any coloring palette that you want with "color byattribute", even though my specific example script replicated the default Chimera "hydrophobicity surface" coloring. See the "palette" option of "color byattribute": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> In general, you can create/assign arbitrary attributes of atoms, residues, chains, etc. using either the "setattr" command to assign one value at a time, or putting a whole series of assignments in an "attribute definition" file and then opening that file. <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html> The ChimeraX mlp calculation is qualitatively and quantitatively different in that it is not a per-residue attribute from a lookup table, but instead calculated based on specific atom types and their 3D coordinates. MLP = molecular lipholicity potential, analogous to ESP = electrostatic potential, and the values are evaluated at or near points on the surface and used for surface coloring. You can also use any coloring palette that you want with the mlp command. What you get by clicking the toolbar icon is just the default mlp coloring. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html> 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 May 29, 2024, at 9:08 AM, Knotts, Garrett via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Good morning,
I am in the process of switching over from Chimera to ChimeraX. I have found ChimeraX to be incredibly more user friendly and well-designed. I wanted to reach out regarding the rangecolor kdHydrophobic command. I often use this command in chimera to color protein surfaces based on hydrophobic character. However, we have a color scheme which our lab has consistently used. In the switch from Chimera to ChimeraX, I have not found a way to color by hydrophobicity with our color scheme using this or other commands, but I have found a way to color hydrophobic regions onto surfaces, without the ability to change the colors. Is there a way to do this in ChimeraX?
Thanks for the help!
Best, ______________________________ Garrett Knotts Undergraduate Lab Assistant (Johnson Lab) Legislative Director of the Mississippi State University Student Association Vice President of Honors Ambassadors Sigma Phi Epsilon Learning Community Coordinator