[Chimera-users] volume viewer question

[Elaine Meng]

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 at 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
>