Thank you Elaine, now I understand better. I was under the impression that using cube files was only consistent with the options related to "volume data". I checked that using an offset of 0 with the electrostatic potential option gives the same result as the volume data value. Related to this: Can I use a cube file to generate an equipotential map? Do you recommend Chimera or ChimeraX? What are the strengths of ChimeraX currently? Best wishes, Christos Deligkaris, PhD Assistant Professor of Physics On Mon, Feb 24, 2020 at 3:22 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Christos, If the option to color by “electrostatic potential” is chosen in the Surface Color dialog, then no matter what kind of volume data file you opened, it has the electrostatic options including offset 1.4 A. You can click Options on the dialog to check that they are all set to the values that you want.
The surface image you gave a link to looks the same to me as the other molecular surfaces in Chimera, in terms of shape. The coloring is too saturated in my opinion (i.e. should have more “white” instead of all blue and red) but that is just a choice of the coloring levels, not related to the shape of the surface. Maybe it was made a long time ago without using an offset, but I don’t know — I didn’t make that image.
If you want to compare what you get using the same settings, and more appropriate coloring levels in my opinion, instead take a look at the image tutorial “coloring by surface properties”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.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 Feb 24, 2020, at 11:57 AM, Christos Deligkaris <deligkaris@gmail.com> wrote:
dear all,
I have obtained a cube file from NWChem with the electrostatic potential around a molecule. I visualized the molecular surface using Actions->Surface->Show and then colored it using the volume data (followed instructions https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html in tools->surface color (electrostatic surface coloring)) .
Since I do not have my data stored in a potential file, can I still do the surface offset? The chimera tool webpage discusses why that is preferred than showing the potential on the solvent excluded surface and it seems to me that option to not be available with volume data.
Also, my surface does not look like the electrostatic potential surface shown here: https://www.cgl.ucsf.edu/chimera/data/tutorials/maps08/volume-basics.html . The molecular surface we get with Action->Surface->Show seems to be constructed with greater atomic radii than the one shown in that image. I am not sure how important that is though. Is there a way to ask Chimera to visualize the electrostatic potential volume data with the same options Chimera would use if it was reading a Delphi, PBS file?
Best wishes,
Christos Deligkaris, PhD Assistant Professor of Physics