Hi Boaz, Here's a video I made showing how to inspect numeric values of electrostatic potential using the mouse and the surfvalues.py script. http://www.cgl.ucsf.edu/chimera/videodoc/SurfaceValues/index.html Tom
Hi Boaz,
Glad it worked. I saved and restored a session and it still worked for me. But I have to reload the script when I restore the session, because it is not saved as part of the session. The numbers are exactly those from the APBS map, just interpolated. I believe APBS uses units of kT/e for those. The surface is made up of small triangles that you can see if you show it as mesh. The APBS values are interpolated for each vertex of a triangle, moved out along the surface normal by 1.4A. When you place the mouse over a specific triangle the values at the triangle corners are linearly interpolated to get the value at the exact point the mouse is at within the triangle.
Tom
Hi Tom,
It works nicely! I gather the surface has to be coloured within the session, then the script works. I tried it first on a restored session in which the surface was coloured previously, but it didn't work. I guess the values are as in the APBS output (kt/e), am I correct?
Thanks again.
Boaz
Hi Boaz,
That's a nice idea. I've put a script surfvalues.py on the Chimera Python scripts web page to do that.
http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts
If you color a surface with an electrostatic potential using the Surface Color dialog (e.g. an APBS potential) then as you move the mouse over the surface the potential values used in the coloring will be shown. By default the Surface Color dialog samples the potential 1.4 Angstroms from the surface so that is the value reported, not the value exactly at the surface point under the mouse. This would be a nice feature to include in Chimera. But I haven't worked out the details -- like how to turn this mouse mode off.
Tom
Hi,
Is there a way to show the actual potential value of a point on the electrostatic surface, say by pointing at it with the cursor, in an analogous way to the atom names that show up that way?
Cheers,
Boaz
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan