[Chimera-users] Showing actual electrostatic potential on surface
goddard at sonic.net
Thu Feb 10 19:08:28 PST 2011
Here's a video I made showing how to inspect numeric values of
electrostatic potential using the mouse and the surfvalues.py script.
> 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.
>> 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.
> Hi Boaz,
> That's a nice idea. I've put a script surfvalues.py on the Chimera
> Python scripts web page to do that.
> 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.
>> 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?
>> Boaz Shaanan, Ph.D.
>> Dept. of Life Sciences
>> Ben-Gurion University of the Negev
>> Beer-Sheva 84105
>> Phone: 972-8-647-2220 ; Fax: 646-1710
>> Skype: boaz.shaanan
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