[Chimera-users] Z-slice transparency
goddard at cgl.ucsf.edu
Tue Nov 6 09:22:13 PST 2007
Here are few more hints for displaying volume data as opaque planes
and also some about movie making.
As I mentioned before you want the yellow brightness/transparency
curve on the volume dialog histogram to be at the top of the histogram.
You also want it to extend all the way from the lowest to the highest
data value. If the lowest node of the curve does is not at the lowest
data value (left edge of histogram) then data values below that lowest
node position will not be shown -- so you will be able to see through
the plane at those low data values.
You may want to add more nodes to the yellow curve. You do this by
holding the ctrl key while clicking with the left mouse button on the
histogram. Ctrl-click on an existing node will delete nodes too.
There is no Chimera command to step through the planes of a volume
that would be helpful for making a movie. But it can be done with a
little Python code. I've attached the 2 line Python script planes.py
that starts and stops plane display. Here's a Chimera command sequence
that would make a movie showing 100 planes:
cd /location/of/planes/script ; movie record supersample 3 ; open
planes.py ; wait 100 ; open planes.py ; movie stop ; movie encode output
You may want to turn off depth cueing (dimming far objects) to get a
brighter plane display. You can use menu entry Tools / Viewing Controls
/ Effects and switch off depth cueing. There is not a Chimera command
to do that. Again a Python script could do it. Or you can setup your
scene including depth cueing turned off, save it as a Chimera session
and then open that session before running a movie making script.
The latest Chimera has a volume command that can be useful for setting
initial thresholds, colors, subregion, ... in scripts.
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