[Chimera-users] Creating and visualizing a plane

[Elaine Meng]

On Sep 24, 2008, at 12:29 PM, Monica Tello wrote:
> I found this very useful, thanks!
> I have been trying to do a similar thing but creating a sphere to  
> put it surrounding the residues in the active site. I tried to  
> create a big water molecule, and this made the trick until I was  
> stuck because I can't change its transparency. Then I thought about  
> creating a marker such as you described for the plane, but I am not  
> familiar with creating these marker files and I am probably missing  
> commands in the .cmm file, because Chimera can't open the file and  
> is giving an error with the info written in it.
> Could you help me out with it?

Hi Monica,
A marker is really just an atom, so that wouldn't make a difference.   
Normally you would use "Volume Tracer" (under Tools... Volume Data) to  
create the marker interactively with the mouse and then save it as a  
file from that tool instead of creating the file with a text-editor.   
I only edited the file in my example so I could specify the  
coordinates exactly. In fact, I created 3 markers interactively, saved  
the marker file from Volume Tracer, and then just edited the x,y,z  
coordinate values.

You can make an atom/marker transparent by creating a transparent  
color and then using it (for example, choosing Tools... Utilities...  
Color Editor, clicking Opacity to include a transparency slider,  
creating the color, and using "colorpanel" as the color name in a  
command or "Actions... Color... from editor" in the menu).
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortool.html>
You can also create and name transparent colors with the "colordef"  
command:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/colordef.html>

Show the atom in the sphere representation; you can change its radius,  
for example by selecting the atom and using a command something like:  
vdwdef 5.0 sel
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html>

In fact, the "Volume Eraser" tool (under Tools... Volume Data) just  
makes a big transparent marker and its dialog has convenient controls  
for changing its color, radius, and position, so you might want to try  
that instead:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html 
 >

Yet another possibility is to make a spherical surface instead of an  
atom/marker.  This can be done with the command "shape":
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html>

You can move that spherical surface relative to your structure and  
change its color just as described for the planar surface in my  
earlier message to Jim.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html