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Hi Boaz,<br>
<br>
Here's a video I made showing how to inspect numeric values of
electrostatic potential using the mouse and the surfvalues.py
script.<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.cgl.ucsf.edu/chimera/videodoc/SurfaceValues/index.html">http://www.cgl.ucsf.edu/chimera/videodoc/SurfaceValues/index.html</a><br>
<br>
Tom<br>
<br>
<br>
<blockquote type="cite">Hi Boaz,
<br>
<br>
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.
<br>
<br>
Tom
<br>
<br>
<blockquote type="cite">Hi Tom,
<br>
<br>
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?
<br>
<br>
Thanks again.
<br>
<br>
Boaz
<br>
<br>
</blockquote>
</blockquote>
<br>
<blockquote cite="mid:4D54472D.9090304@sonic.net" type="cite">
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Hi Boaz,<br>
<br>
That's a nice idea. I've put a script surfvalues.py on the
Chimera Python scripts web page to do that.<br>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts">http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a><br>
<br>
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.<br>
<br>
Tom<br>
<br>
<blockquote cite="mid:fa1387576b58.4d53ff04@bgu.ac.il" type="cite">Hi,<br>
<br>
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?<br>
<br>
Cheers,<br>
<br>
Boaz<br>
<br>
<br>
Boaz Shaanan, Ph.D.<br>
Dept. of Life Sciences<br>
Ben-Gurion University of the Negev<br>
Beer-Sheva 84105<br>
Israel<br>
Phone: 972-8-647-2220 ; Fax: 646-1710<br>
Skype: boaz.shaanan<br>
<br>
<br>
</blockquote>
</blockquote>
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