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...

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@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