Hi Nihshanka, It is necessary to delete atoms you don't want included in the calculation before initiating the calculation. Undisplaying atoms or surface does not make a difference - the atoms are still there, just undisplayed. Later, you could open the electrostatic potential map with the original full structure, if you wanted to display parts that had been deleted for the potential calculation. The "Electrostatic Surface Coloring" tool does get a potential value at each surface point in order to do the coloring, but the values are not available from the user interface. The "Values at Atom Positions" tool could be used to get the potential at the positions of atoms, but not the surface. If you knew particular coordinates you wanted to look at, you could make a PDB file with fake atoms at those positions and use the latter tool. However, if you really did want all the surface point values, I must defer to others who know python and the under-the-hood details. Electrostatic Surface Coloring man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/ surfcolor.html Values at Atom Positions man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/density/ density.html Best, Elaine On Aug 6, 2006, at 11:36 PM, Nihshanka Debroy wrote:

Hi everyone, I have a couple of questions about the electrostatic potentials generated in Chimera using the Delphi Controller. If I have a protein with 5 chains A,B,C,D,E, and I choose to show the surfaces of all chains except C (but keep the wireframe of chain C's atoms) and then run Delphi using the DelphiController, does that mean that the potential surface generated is in the absence of chain C (which is what I want)? I'm trying to generate the potential surface without taking into account chain C, but would like to see C's wire frame for analysis purposes. Also, is there a way to get the actual potential values at each surface coordinate?

Thanks a lot for the help. Sincerely, Nihshanka _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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 chimera/share/Surface_Color/__init__.py 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 again. 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. Tom