Chimera User's Guide, the coloring of the MSMS surface using red, blue and white is described: "The Molecular Surface option allows coloring by electrostatic potential at the molecular surface (as in the figure above). Positive potentials range from white to blue, and negative potentials range from white to red. Potentials at or above the cutoff value are fully blue, and potentials at or below the negative of the cutoff value are fully red. The white area is transparent in MSMS surfaces, opaque in Grasp surfaces." The Chimera help menu has a User's guide entry that will show this stuff in a web browser. As you note, the areas of low potential really look gray, and dark gray not white. This is because they are set to be a very transparent white and the black background of the Chimera window shows through. To see this you can go to Settings/Preferences category Background and change the background color to white. That makes the low potential areas look white, but you probably don't want a white background. Eric Pettersen has added color buttons to the DelphiViewer user interface so you can change the red, blue, and white colors, including the transparency, and this will be in the next release. What you want is probably to make the white less transparent. You can do that in your current Chimera 1602 by editting a file. Look at /usr/local/chimera/share/DelphiViewer/MSMSTexturer.py near line 78 you'll find red = chimera.MaterialColor(1, 0, 0, 0.9, None) white = chimera.MaterialColor(1, 1, 1, 0.1, None) blue = chimera.MaterialColor(0, 0, 1, 0.9, None) This is setting the colors, red, white, blue, and transparency values each on a scale of 0 to 1. For the transparency 0 means completely transparent and 1 means completely opaque. So if you change these lines to red = chimera.MaterialColor(1, 0, 0, 0.9, None) # white = chimera.MaterialColor(1, 1, 1, 0.1, None) white = chimera.MaterialColor(1, 1, 1, 0.9, None) blue = chimera.MaterialColor(0, 0, 1, 0.9, None) and restart Chimera, you'll get white low potential regions. Here the "#" is the comment character in the Python language. I can ask Eric if the unreleased DelphiViewer with the color buttons on the user interface will work in Chimera 1602, and try to get that to you so you don't need to edit the file. Tell me if you want that. You say the MSMS surface looks incomplete. Can you tell me a specific PDB file and atom to look near to see the problem? The MSMS probe radius is set to 1.4A. You can see this by using Controllers/Model Panel, click on the line for the MSMS surface, and press the Attributes button. Normally you can edit the probe radius and press enter and it will automatically update the surface. But when I tried this with Delphi coloring I got an error and had to close the MSMS surface to get the graphics window to display anything again. If I change the probe radius before doing the Delphi coloring the surface is recalculated with no error. Tom

From: "Wade Nasholds" <vesuvius@omantel.net.om> To: "Thomas Goddard" <goddard@cgl.ucsf.edu> Subject: DelPhi in Chimera Date: Fri, 14 Feb 2003 21:08:41 +0400

Hello Tom, Thanks for your previous email. Certainly helps. I got build 1602 of Chimera (thanks) and have tried it with some DelPhi .phi files that I've generated. I've been able to render MSMS surfaces showing electrostatic potentials successfully. This is great news because that's what I've been aiming to do! The potential extremes are shown in red & blue but the intermediate potential shows as shades of light grey to dark grey rather than the expected white (neutral). Also, the molecular surface seems incomplete in certain spots. I don't think it is a matter of DelPhi parameter settings, as I've tried different ones but to no avail. Although it still may be due to DelPhi settings still unknown to me as I'm still learning how to use it. Might it be something to do with Chimera? I've altered the kT/e settings in DelPhi viewer but it hasn't resolved the problem.

Is the default surface probe (water) set at 1.4A in the MSMS feature of Chimera?

Thanks again for your time. Wade