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

Hi Jéromine, The SASA values you get are literally the square angstroms of solvent-accessible surface area of that set of atoms, in the context of the larger structure. If you are tabulating these values per residue to decide what is buried and exposed, there are some possible additional considerations. A simplistic approach is to just have a cutoff and say all residues with greater than that value are exposed. I don't have a number you should use, it is a judgment call where you can try different values until the results seem reasonable for your purposes. However, because different residues are different sizes, some people are interested in normalizing the values so that you get a % exposed compared to some totally exposed reference state of that same residue. A fully exposed alanine (small) will have a smaller SASA than a fully exposed phenylalanine (large), for example, and you wouldn't want to classify all surface alanines as buried just because they are small. But ChimeraX does not do the normalization for you, nor do we have a set of values for fully exposed amino acids. Some people have used an extended Gly-X-Gly tripeptide as the reference state for fully exposed (where X is each type of amino acid), but without somebody else having shared their values, you would have to make all these reference states and measurements yourself. You can't necessarily use some published set of these "denominator" values since it depends on all of the atomic radii used in the calculation; they'd have to use the ChimeraX radii, assuming that's what you are using when getting the "numerator" values. This was discussed in a previous post: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> For Chimera, we did have a set of "denominator" values but they were for SES (solvent-exposed surface), <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html> ...unfortunately not for the SAS (solvent-accessible surface) which is the only one that ChimeraX calculates. If you're not clear on the difference between SES and SAS see the diagram here: <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> I hope this clarifies the situation. Best, 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 Oct 21, 2025, at 2:19 AM, Jéromine Carret via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello Elaine,

Thank you for all your information and the helpful links you sent me.

I think we'll stay in the visual results for the facility. Besides, I have a few one more question about burial and its interpreation.

We looked into the burial status, and the ‘sasa’ command appears to be useful for that purpose. I found some information in Fischer et al. (2006) about calculating the delta SASA and determining whether a residue is more exposed or buried. Do you have any guidance on how to interpret the results provided by ChimeraX and understand their meaning?

Thanks for all your help!

Kind regards,

Jéromine

----- Mail original ----- De: "Elaine Meng" <meng@cgl.ucsf.edu> À: "Jéromine Carret" <jeromine.carret@univ-lille.fr> Cc: "chimerax-users" <chimerax-users@cgl.ucsf.edu> Envoyé: Jeudi 9 Octobre 2025 19:26:52 Objet: ways to compare protein variants

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

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