Hello, There is command "color byattribute" and you need to give the name of the attribute "seq_rmsd". For the RMSD attribute to be assigned to residues, you need to have the RMSD header shown on a sequence alignment window, and the structures associated with a sequence in that window.
color byattribute command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute
However, the easier way may be to use the graphical interface, menu: Tools... Structure Analysis... Render by Attribute. You still need to have the sequence alignment with RMSD header as above, but then in this Render by Attribute tool you can choose attribute of "residues" named "seq_rmsd" and set the coloring how you like. This will show the resulting command in the Log so later you can just use the command instead of the tool if you prefer.
How to do it is shown in a video: https://www.youtube.com/watch?v=XaTpB-UIxnU
Render by Attribute tool: https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.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 Feb 26, 2024, at 8:21 PM, 林萌萌 via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
What's the command for “colored by atoms by rmsd” ？