[chimera-dev] volume display with transparency

[Thomas Goddard]

  Steve asks about transparency with _surface and PDB models.

	Tom

------- Start of forwarded message -------
Date: Tue, 20 May 2003 22:45:43 -0500 (CDT)
From: Steve Ludtke <stevel at blake.3dem.bioch.bcm.tmc.edu>
Reply-To: sludtke at bcm.tmc.edu
To: Thomas Goddard <goddard at cgl.ucsf.edu>

Hi once again. Making very good progress (unfortunately I've got limited 
time to spend on this diversion). Anyway, run into a couple more 
questions. This time wrt volume data and transparency. Once of the effects 
I'm looking for is to 'fade in' an isosurface using transparency. First, 
the 'bug'. When the transparency is fully on, ie - 100% transparent, the 
surface hilights are still visible. The lighting model doesn't seem to 
fully take this into account. On the Volume Viewer panel, there is a 
'Transparency Factor' slider. It's also possible to change the alpha of 
the surface color. Changing one has no effect on the other, and it's not 
quite clear to me how they are related. A similar question for the 
'Brightness' slider. It's also a little distracting how the current 
lighting model makes the volume oversaturated when transparency is used 
unless the color or brightness is also varied.

Programmatically I didn't find any volume viewing info in the headers you 
sent. What I'm looking for is a code snippet that, given the 
chimera.openModels.list()[x] object, how can I set Brightness, 
Transparency Factor, Color and isosurface level. I seem to recall asking a 
similar question a very long time ago, but I think I lacked a context at 
that time.

One last question, which I fear the answer to is "you can't". I'd also 
like to be able to fade in and out molecular models. Any way to get 
transparency to work on PDB renderings ?

Thanks as usual  :^)


- -- 
- ----------------------------------------------------------------------------
Steven Ludtke, PhD              |        Baylor College of Medicine
sludtke at bcm.tmc.edu             |               Co-Director
stevel at alumni.caltech.edu       | National Center For Macromolecular Imaging 
V: (713)798-6989                |    Dept of Biochemistry and Mol. Biol.
instant messenger: sludtke42    |            * Those who do ARE *
http://ncmi.bcm.tmc.edu/~stevel |           The converse also holds
------- End of forwarded message -------