Hi JPD, See command "measure mapValues" to assign such an attribute: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapValues> ... often if you look at the help page for some tool, it will crossref to the corresponding command (if any): <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html> However, it does not automatically save to an attribute file. In Chimera, you still have to do that manually from the Render by Attribute menu (there is no command), as described at the bottom of this page: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving> If you would consider switching to ChimeraX from Chimera, it also has a "measure mapvalues" command, and it allows you to save an attribute file with the "save" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#mapvalues> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> 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 Nov 1, 2024, at 3:23 PM, jp d via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

hi, sorry to bother you again, is it possible to run "Values at Atom Postions" from a script where i specify map,pdb and just the output attribute file ? thanks jpd