Hi Steve, ChimeraX is a 3D visualization program. So documentation that refers to "contour plots" means 3D contour surfaces. There is little capablity for 2D contour line visualization or measurements restricted to planes, but that can be done in cumbersome ways. Here's an example, making 2D contours using mesh display with a single plane of data. I'm using an EM databank map since I don't work with Gaussian files, but the method applies to any 3D volume data that ChimeraX can open. open 63190 from emdb volume #1 plane z,132 style mesh cap false level .3 color red level .6 color orange level .9 color yellow level 1.2 color green level 1.5 color blue level .1 color white open 9ll0 hide #2 ribbon ; show #2 atoms clip front 6 back 10 position 108,108,104 axis z coord #1 You could measure distances by placing markers. I absolutely would not use ChimeraX for this kind of 2D visualization as it will be very tedious since the program is not designed for 2D. Tom
On Jan 7, 2026, at 6:42 PM, Steven Brawer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I have used Chimerax for proteins, and it is indeed wonderful.
However, now I would like to use it to view output from the Gaussian16 "computational chemistry" program, and I am at a loss. I believe the "volume" command is what I need, but I have a LOT of trouble understanding the terminology of the user documentation for the "volume" command.
Perhaps someone can be very specific and guide me in the particular procedure described below (or tell me Chimerax does not do such a thing).
I have a Gaussian16 cube file for electron density. (This is electron density on grid points. Chimerax can read this file.) I would like to make a contour plot - say contours in the xy plane at z = 0. I would like to specify the number of contours. I would like to know the distance (in au units) of any point on a particular contour from the origin (x=y=z=0) or even from some arbitrary point in space. I would like some sort of legend indicating the density value of each contour. How can I set this up?
It would also be nice to be able to specify any plane.
Thanks very much
Steve _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
