[Chimera-users] Creating and visualizing a plane

James Nettles jnettle at emory.edu
Tue Sep 23 18:43:59 PDT 2008


You and Chimera are fantastic resources.

With highest regard,


Molecular graphics images were produced using the UCSF Chimera package  
from the Resource for Biocomputing, Visualization, and Informatics at  
the University of California, San Francisco (supported by NIH P41  

Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt,  
D.M., Meng, E.C., and Ferrin, T.E. "UCSF Chimera - A Visualization  
System for Exploratory Research and Analysis." J. Comput. Chem. 25(13): 
1605-1612 (2004).

On Sep 23, 2008, at 8:00 PM, Elaine Meng wrote:

> 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
> <tripod.cmm>
> <square.cmm>


James Nettles, Ph. D.  Assistant Professor
Department of Pediatrics, Emory University School of Medicine
Laboratory of Biochemical Pharmacology (LOBP)
Computer Assisted Discovery Research Environment (CADRE)

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