[Chimera-users] Creating and visualizing a plane

[Elaine Meng]

On Sep 23, 2008, at 1:08 PM, James Nettles wrote:

> I'm not sure if this is a function available in Chimera.
> I have a protein system with three residues which define a plane, or  
> floor, relative to an active site. I would like to display a  
> translucent plane passing through the alpha carbon of these three  
> residues to shoot an image. Further, I would like to quantify   
> deviation of mobile regions relative to this plane.
> Thanks,
> Jim


Hi Jim,
It can be done, but the route is currently a bit circuitous:
(1) place points to define a surface
(2) generate surface
(3) make surface transparent
(4) select atom in structure, measure distance to surface

Although we plan to create tools for conveniently defining axes,  
planes, and centroids for specified sets of atoms and performing  
various measurements on them, so far only the Axes part has been  
implemented.  Hence this more circuitous procedure...

(1) Placing points.
I was initially going to say what you wanted couldn't be done without  
python, but realized that the Volume Tracer tool can create surfaces  
from arbitrary sets of points, or "markers" (actually they are handled  
much like atoms in Chimera).  I tried two approaches to making markers:

(a) simply creating a Chimera marker file "tripod.cmm" containing  
three markers with the same coordinates as three active site atoms in  
an example structure (2gbp, near ligand glucose or residue GLC) -  
these will automatically coincide with the atoms.  The marker file is  
a small, simple text file.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html 
 >
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#markerfiles 
 >

(b) creating a Chimera marker file "square.cmm" with four markers at  
(0,0,0) (0,50,0) (0,50,50) (0,0,50) to make a big square that that can  
be positioned manually relative to the structure

You can also create markers interactively with the mouse, but it is  
not easy to control their exact coordinates that way.  That is why I  
just text-edited to create the marker files (attached for your  
convenience).  You could take my three-point file and edit in the  
coordinates to match your three alpha-carbons if it is OK that the  
surface is only a triangle connecting those points.  However, if you  
wanted a larger plane that would extend further, instead open the four- 
point file for making a big square and later position it relative to  
your structure.

(2) Generating the surface.
After you open the marker file (*.cmm) in Chimera it will just be  
shown as an unfilled triangle or square.  Ctrl-click to select one of  
the corner markers (just as if it were an atom), hit keyboard up arrow  
so that all three or four are selected.  In the Volume Tracer dialog  
(Tools... Volume Data... Volume Tracer), choose Features...Surfaces  
and click the Surface "Create" button.  Now the triangle or square is  
filled and another model named "Traced surfaces" is listed in the  
Model Panel.  You can close the model containing the markers since it  
is no longer needed.  Also close the Volume Tracer dialog if it is  
still open.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#surfaces 
 >

(3) Making the surface transparent.
Ctrl-click on the surface to select it and open the Selection  
Inspector (for example, with Actions... Inspect).  In there, you can  
inspect "Surface piece" and click the color well to edit the color.   
In the color editor, check "Opacity" to get another slider that  
controls the transparency of the color.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortool.html>

(4) Measure distances to the surface.
First you may need to manually position the surface relative to the  
structure.  You can freeze/unfreeze the different models (whether they  
are movable with the mouse) using the "Active" checkboxes under the  
Command Line or in the Model Panel.  When it's in the right place, you  
can select an atom and then use the command "ac sd" to measure its  
distance.  ("sd" is really a keyboard shortcut but can be embedded in  
an "ac" command to avoid having to go into shortcut mode).
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ac.html>

Phew!  I will send you an image in a separate message.  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

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