Hiscaro, I played around with your files a bit, and I found that the isosurfaces at 0.01/-0.01 look pretty similar to what's in the orca documentation. The orca page doesn't mention what they set the contour value to, so I'm not sure if this is exactly the same. I also recalculated the cube files with orca_plot using a 100x100x100 grid, as the default 40x40x40 was coarse enough that I had trouble seeing the smaller lobes. Here's the command I used to set the isosurfaces and colors: volume #5 level -0.01 level 0.01 color #0000ff5c color #ff00005c (the result of the volume subtract command was in model #5) I've attached images showing the fukui functions with these settings. If you have any other questions, let me know. Best, Tony On Wed, Jan 14, 2026 at 11:48 PM fsl--- via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello all,
I'm trying to calculate Fukui functions [1] using orca, I'm trying to recreate the plots mentioned in [1] as well. Briefly, I have generated two surface files f_n+1.cube and f_n.cube. I tried running in ChimeraX's console
``` open f_n+1.eldens.cube format cube open f_n.eldens.cube format cube volume subtract #1 #2 ```
But I get is a histogram on side with the level slider, and none of the levels match with the output figure on [1]. I'm not sure how to proceed ahead.
Am I missing something, isn't there a surface subtract? rather than volume subtract. The files I used for the plots are in [2].
Regards hisacro.
[1]: https://www.faccts.de/docs/orca/5.0/tutorials/react/FUKUI.html [2]: https://displ.nl/pb/lactone2.tar.xz _______________________________________________ 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/
