Hi, Your command is making the molecular surface completely invisible (100% transparent). It also creates a map, so what you are seeing is the default positive and negative isosurfaces for a signed map, with initial isosurface levels determined automatically, which will always be the same for the same map. Do you need this separate map model for some reason? If you just want to color the molecular surface then don't bother creating a separate map model, just try something like mlp #1 key true palette lipophilicity range -5,5 or to avoid the oversaturation I see with the above, just use default coloring mlp #1 key true See "mlp" help page with command "help mlp" or view the copy on our website here: <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 Aug 4, 2025, at 4:11 PM, Roy Chowdhury, Shatabdi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I'm trying to display the hydrophobic parts of a molecule, and I'm trying this command "mlp #1 map true key true palette lipophilicity range -5,5 transparency 100"
When I use various values for the lipophilicity range, it does not affect the colors of the potential. They also do not have the gradients like the molecule display -> hydrophobic tab.
Is there a way to make this happen? Thanks,
Shatabdi Roy-Chowdhury, PhD. Postdoctoral Research Scholar, Cardiovascular Research Institute University of California, San Francisco