[Chimera-users] Showing actual electrostatic potential on surface

[Tom Goddard]

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
>>
>> ‎

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