Hello Jéromine, I changed the subject line to something more descriptive since basically everything here is a question about ChimeraX. :-) Many of these tools are primarily for interactive visual analysis, not for getting some specific quantity or number. If you try to boil the results down to specific numbers they may not be that meaningful compared to interactive visualization, because the results are inherently 3-dimensional and complex. For example, the purpose of Matchmaker is to superimpose the proteins as well as possible for comparisons, or sometimes transplanting ligands or symmetry partners. yes you can look in the Log to see the resulting RMSD and number of alpha-carbon pairs used in the final fit, but that is only secondary to the main purpose of superimposing the proteins. You can also use the option to show the sequence alignment to better understand how residues were paired and which pairs were used in the final fit, as described in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#alignment> Similarly, the Coulombic electrostatic calculation and molecular lipophilicity calculation are best understood by showing the values at the molecular surface as coloring, since at the surface is where they potentially interact (no pun intended) with other molecules. Whether you "avoid coloring" is orthogonal to creating the values on a 3D grid to make a map, and I would say that coloring is generally the most meaningful way to understand the results. You can generate maps with: "coulombic" command with "map true" - see help for details <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coulombic.html> "mlp" command with "map true" - see help for details <https://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html> ... and then save the map model to file, see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map> For your other question, there is a Clashes tool and you could start by using the default parameters for what is considered a clash: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> See also the tutorial "Protein-Ligand Binding Sites" for frequently used structure analysis tools: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 9, 2025, at 5:51 AM, Jéromine Carret via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
My name is Jéromine, and I am a PhD student at the University of Lille, France. We are working on structural modelling of different protein variants. We have questions about the ChimeraX software tools.
We would like to obtain electrostatic maps of protein structures and avoid using the colour scale in order to obtain numerical results. And also for hydrophobicity maps.
We also want to study the clashes between the positions of variants. Do you have any advice?
For the matchmaker command, can you give me the information I need to understand the results?
Thank you in advance for your reply.
Kind regards.
Jéromine Carret PhD candidate RADEME lab ULR 7364 Université de Lille