Hi Megan, I guess you mean ChimeraX (not Chimera). They are two different programs, but only ChimeraX has MLP calculations. If I understand correctly: since the maps and the surface are all generated based on the same set of atomic coordinates, they should already align with those coordinates and thus also with each other. I.e. if you open them all again and use them to color the molecular surface with the same palette, it should look the same as it did originally. Note, however, that these MLP and ESP maps are meant for visual analysis by coloring on the molecular surface to understand in general where it is more/less hydrophobic and positive/negative for interacting with other molecules, but not for any quantitive comparisons of the grid values point by point. So if you meant you needed the grid points to be in exactly the same locations, there isn't direct control over that, but I question the utility of any calculations that would require them to be. You can resample one map to the grid of another map so that they are on exactly the same points, but that interpolates the values, and again I'm not sure why you would want to do it. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#resample> Or, if you mean you are comparing maps made from different structures, you may need to superimpose the structures first, then save PDB files of the reoriented coordinates relative to one another, and then reopen those files before calculating maps etc. I'm also not sure what calculating SASA has to do with the coloring of the molecular surface. The displayed molecular surface in ChimeraX is not the SAS, as explained here <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.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 Jan 31, 2025, at 4:41 PM, msteves--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello, I'm new to Chimera, but would like to use it to generate surface maps of electrostatic potential and hydrophobicity, then output for further analysis. I've generated maps using coulombic and mlp commands, and successfully saved these to .MRC format. However, when I go and read these files, the dimensions of the maps are different, so I'm not sure how to properly overlay these maps in my later analysis. Is there a way to have Chimera generate maps only within a given spatial range, so I end up with maps of the same size? Or another way you would recommend going about this?

In later analysis I'd also like to make use of the SAS calculated by Chimera, and I imagine I will also have difficulties properly aligning the surface to the maps, so any advice on this would also be greatly appreciated!

Thanks, Megan Steves