[Chimera-users] Coloring nucleic acid ladder with opacity. Possible bug?

Tom Goddard goddard at sonic.net
Tue Oct 9 18:11:48 PDT 2012

Hi Rebecca,

   Transparency does not work well with Chimera's nucleotide 
representations (slabs, ladder).  Here's a technical explanation that 
may help you understand why you see what you see.  The transparent 
nucleotide ladder is shown by multiplying the red, green, blue color 
components (range 0 to 1) by the opacity (= 1 - transparency) and those 
color values are simply added to the image.  Even in single-layer 
transparency mode both the back and the front of the cylinders are being 
added which makes the colors twice as bright as they should be and can 
make it appear entirely white if rgb values all end up greater than 1.

   This is a defective way to show something transparent. Nucleotides 
are drawn as "VRML" models and all such Chimera models have this 
deficiency.  Normal surfaces and molecules in Chimera do not have this 
problem with transparency.  It may be possible to fix the VRML 
transparency so it respects the "single-layer transparency" option and 
that would make it much better since front and back side colors would 
not get added creating an overly bright (sometimes white) appearance.


-------- Original Message --------
Subject: Re: [Chimera-users] Coloring nucleic acid ladder with opacity. 
Possible bug?
From: Greg Couch
To: Rebecca Swett
Date: 10/9/12 5:31 PM
> It's not a feature. :-)  For me, transparency for ladder rungs kinda 
> works -- the rungs are transparent, but not enough.  And I only see 
> opaque white when the ladder rungs are facing the key light. You could 
> mitigate the opaque white by moving the model or the key light.  If 
> you are seeing different results or if you're interested in being 
> notified after the bug is fixed, please file a bug report.
> FYI, in the Chimera daily build (available tomorrow), I've eliminated 
> the extra cylinder caps that are exposed when you make the ladder 
> transparent, so you can get a slightly better picture.
>     HTH,
>     Greg
> On 10/07/2012 07:01 PM, Rebecca Swett wrote:
>> Hey all, quick question on coloring here. I'm handling a structure 
>> that has nucleic acids and protein. I'd like to represent the nucleic 
>> acids with the ladder representation and then have them at a lower 
>> opacity to bring focus to the protein structure. When I try coloring 
>> the ladder with opacity, the ribbons color just fine, but the rungs 
>> go opaque white. Is this a bug, or has anyone gotten this to work? I 
>> just updated to 1.6.2. Thanks for any help.
>> ~Rebecca
>> Rebecca Swett
>> Wayne State University
>> 357 Chemistry
>> Detroit, MI 48201
>> Lab Phone 313-577-0552
>> Cell Phone 906-235-0768
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