[Chimera-users] Coloring nucleic acid ladder with opacity. Possible bug?
goddard at sonic.net
Tue Oct 9 18:11:48 PDT 2012
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.
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.
> 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 Swett
>> Wayne State University
>> 357 Chemistry
>> Detroit, MI 48201
>> Lab Phone 313-577-0552
>> Cell Phone 906-235-0768
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