[Chimera-users] Creating and visualizing a plane
meng at cgl.ucsf.edu
Wed Sep 24 13:24:59 PDT 2008
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?
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
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).
You can also create and name transparent colors with the "colordef"
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
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
Yet another possibility is to make a spherical surface instead of an
atom/marker. This can be done with the command "shape":
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 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
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