[Chimera-users] Electrostatic Potentials

Thomas Goddard goddard at cgl.ucsf.edu
Mon Aug 7 17:22:17 PDT 2006

Hi Nihshanka,

  If you want to just dump all the xyz coordinates of the surfaces
points and the electrostatic potential you could modify the Chimera
code in a small way.  You would modify file


using any text editor.  After line 157

    def point_colors(self, vertices, vertex_xform):

        values, outside = self.volume_values(vertices, vertex_xform)

add the "for" and "print" statements shown below.

    def point_colors(self, vertices, vertex_xform):

        values, outside = self.volume_values(vertices, vertex_xform)
	for i in range(len(values)):
	   print vertices[i], values[i]

Indentation is important so indent as shown.  This change will print
each xyz coordinate and the potential value to the Chimera reply log
(menu Favorites / Reply Log).

  Printing a huge list of surface points and potential values may not
be that useful since it will be hard to determine what atoms the
surface points are near.  Here is a differnt approach to check the
potential at specific points.  The basic idea is to place a marker and
move it to where you want to know the potential.  Place the marker
using volume path tracer, menu entry Tools / Volume Data / Volume Path
Tracer.  Turn on the switches "Drop markers on empty space" and also
"Move markers with mouse" in the path tracer dialog.  Then click with
mouse button 3 with the Ctrl keyboard key held down to drop a marker.
You can drag the marker using Ctrl-button-3 to whatever location you
want.  Now use the Values at Atom Positions tool, menu entry Tools /
Volume Data / Values at Atom Positions.  Select "marker set 1" from
the Molecule menu.  This is the fake molecule that contains the marker
you just dropped which is a fake atom.  Now press the Histogram button
on the values at atom positions dialog.  That will show another dialog
giving the potential value at the marker position.  To get the value
at a new position, drag the marker and press the Histogram button

  Would be nicer to be able to just click on the surface to get the
potential value at that surface point.  That is not currently possible
but I'll add to my list of requested features.


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