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

Tom Goddard goddard at sonic.net
Wed Oct 10 10:04:13 PDT 2012

Hi Rebecca,

I put in a fix so that nucleotide ladder transparency looks right in 
tonight's daily builds.  The fix applies to all Chimera VRML models when 
single-layer transparency is used.  If multi-layer transparency is used 
then the opacity times the red,green,blue values of all transparent 
layers are added together without regard to which layers are in front of 
which other layers, and that will still produce overly bright and 
incorrect transparency.  That is hard to fix.  The single-layer 
transparency mode is the default in Chimera 1.6 and later.


-------- Original Message --------
Subject: Re: [Chimera-users] Coloring nucleic acid ladder with opacity. 
Possible bug?
From: Tom Goddard
To: Rebecca Swett
Date: 10/9/12 6:11 PM
> 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.
>     Tom
> -------- 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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