[Chimera-users] Opaque volume planes

William Jeffrey Triffo triffo at rice.edu
Tue Feb 12 17:47:37 PST 2008


do you know when tonight's builds will go through, I will test it at 
that point to see if the functionality made it in


Tom Goddard wrote:
> Hi Jeff,
>  The trouble obtaining opaque volume planes is not related to volume 
> plane display being built into the volume dialog.  It is related to a 
> change I made in how transparency is handled in solid mode back in Aug 
> 2007.
>  Today I changed transparency in "solid" style volume rendering so it 
> is easier to obtain completely opaque data planes.  In tonight's 
> builds (if they succeed, may not since we are switching to Python 2.5 
> today) you can obtain completely opaque volume planes by using the 
> "Brightness and Transparency" panel of the volume dialog to set 
> transparency to 0.  This transparency value represents the fraction 
> (0-1) of the depth of the volume required to produce opacity to the 
> degree indicated by the height of the yellow curve on the histogram.  
> In other words it modulates the overall transparency.  But until today 
> it was arbitrarily deciding not to modulate the transparency if this 
> depth was less than one grid spacing.  This meaning of the 
> transparency factor was introduced in August 2007, and prior to that 
> the transparency factor just scaled the opacity given by the yellow 
> curve.
>    Tom
> Jeff wrote:
>> hi Tom,
>> in the older (plug-in) volume planes tool, I was able to generate 
>> images that were opaque planes. I don't seem to be able to do this 
>> anymore, even with transparency = 0. is there a way for me to do this 
>> in the current Chimera?

Jeff Triffo
Auer Group, Donner Lab, Lawrence Berkeley National Laboratory
Raphael Group, Bioengineering Department, Rice University
Medical Scientist Training Program (MSTP), Baylor College of Medicine
phone (Berkeley): 510-486-7940
fax   (Berkeley): 510-486-6488   

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