Hi Ben, Your short questions require long answers! (1) viewing DOCK scoring grids. Just to clarify for everybody, I believe you are referring to the DOCK scoring grid calculation program, not the separate and more famous GRID program (whose output is currently not read by Chimera). My tests today used DOCK grids I made a few years ago, but I am told their format has not changed. Opening the *.nrg grid file shows three separate histograms in Volume Viewer: electrostatic, vdw attract, and vdw repel. Each is initially shown with a single contour surface, and you can change the contour level by dragging the vertical bar on the histogram. Volume Viewer documentation: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ volumeviewer/framevolumeviewer.html> Since Volume Viewer has so many features, I will step you through the ones that seem relevant. Qualitatively, both the vdw datasets mainly show where the receptor atoms are. Since you mentioned you are looking at electrostatics, just close both the vdw datasets by clicking the "minus sign" button to the right of their respective histograms. Then you are left with just the electrostatic histogram. Although it initially just has one contour surface, you can have multiple contour surfaces - Ctrl-click the histogram to add contour levels (shown with vertical bars or "thresholds"), which can then be colored differently (more on this below). You probably want at least one negative contour and one positive contour. However, by default when there is a negative contour it just shows the outside of the grid box, so there is another option that needs to be set: from the Volume Viewer Features menu, choose "Surface and Mesh options" to show additional options in the dialog. Then turn off the "Cap high values at box faces" option. You can hide that section of the dialog again if you want by clicking the "X" button to the right of "Surface smoothing iterations." <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ volumeviewer/volumeviewer.html#dispsurf> Clicking the square Color well for the most recently added or moved threshold allows you to edit its color. Click the Opacity button on the color editor if you want to make the color transparent. Another possibility is to change the Style in Volume Viewer to mesh. Now adjust the contour levels as desired by dragging the vertical bars on the histogram, and then open the receptor and possibly also ligand files for viewing together with the electrostatics grid. I believe the electrostatic grid values are Coulombic electrostatic potential, but exactly how they are calculated depends on your grid- calculation input parameters, so you would need to consult the DOCK manual for further details. (2) showing 2D contours (lines). To do this part you need a recent daily build (newer stuff than the production release). The steps above get you to the point of showing "blobs" of negative and positive potential. However, you can show lines by showing just one plane of the electrostatic grid at a time. Essentially this is a very thin slice through the blobs. To do this, from the Volume Viewer Features menu, choose "Planes" to show planes options in the dialog. In that Planes section of the dialog, you can edit "Depth" to 1 (one plane), move the slider to control which plane is shown, and change which axis is used. You can also click the "One" button to show just a single plane at a time. It may change the Style to "solid" but if it does, just switch it back to "surface" to show the lines. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ volumeviewer/volumeviewer.html#planes> (3) electrostatic potential calculations in Chimera. Currently Chimera does not calculate electrostatic potential, but reads in electrostatic potential maps that the user has generated separately with one of the following programs: DelPhi, GRASP, APBS, UHBD. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> Opening any of those file types automatically starts "Electrostatic Surface Coloring" since people more commonly color the molecular surface by potential than show isopotential contours. Note you could also use this tool with the electrostatic part of the *.nrg scoring grid. To do that, undisplay the contours by clicking the little oval "eyeball" above the histogram in Volume Viewer (but do not click the minus sign, which would close the data), display a molecular surface, start Electrostatic Surface Coloring (under Tools... Surface/Binding Analysis), and proceed as described: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/ surfcolor.html> However, if you do want to show contours, just close that tool, open Volume Viewer (under Tools... Volume Data), click the little "closed eyeball" icon above the histogram to display the contour surface, and proceed as described in (1) and (2). Finally, I should mention we are working on a new Chimera tool to calculate Coulombic electrostatic potential and use it to color molecular surfaces, but it is not done yet. However, as mentioned above, you already have this type of potential included in your *nrg grid file. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Oct 3, 2008, at 9:36 AM, Ben Keshet wrote:
Hi Chimera fans, Can someone please help me understand how to read and look at .nrg files (generated by Grid)? I am interested in visually exploring the electrostatic potential around a protein. Specifically, when I opened it, everything was in one color, with negatively charged regions being darker, but I would imagine that positively charged regions should have a different color. On a related note - is there a tool to calculate and view the electric field lines around a molecule / protein? Thanks for your time and help, Ben