[Chimera-users] Z-slice transparency

Tom Goddard goddard at cgl.ucsf.edu
Tue Nov 6 09:22:13 PST 2007

Hi Lu,

  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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