[Chimera-users] Electrostatic Potentials

Thomas Goddard goddard at cgl.ucsf.edu
Tue Aug 8 18:31:30 PDT 2006

Hi Nihshanka,

  Oops!  My previous descriptions of how to determine electrostatic
potential values at specific surface points assumed you were using
the Surface Color tool to display the potential (menu entry Tools /
Structure&Binding Analysis / Electrostatic Surface Coloring, or menu
entry Tools / Volume Data / Surface Color).  But you are using
DelphiController and it has its own code for displaying potential
values for which my previously described techniques will not work.

  To print the potential values at every surface point when the potential
display was done with Delphi Controller you could put a print statement in


at line 155, after the following lines of code

				# Point is outside of phi map.
				phivalue = 0
add the line

			print v_rs, phivalue

Make sure the "print" line is indented the same as the "else:".
This is going to print many thousands of lines in the Reply Log so
be prepared to wait a bit.

  You could also use my previously described methods for showing
potential values by using the Electrostatic Surface Coloring tool.
Show a surface for your PDB model using Actions / Suface / show.  Then
in the Electrostatic Surface Coloring dialog press the "Open map
data..."  button and select the *.phi file generated by DelPhi (the
one computed when running Delphi Controller).  Then press the Color
button on the surface color dialog.  My previous code modification
or the marker probe method could them be used.


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