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

Greg Couch gregc at cgl.ucsf.edu
Tue Oct 9 17:31:20 PDT 2012

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
> Rebecca Swett
> Wayne State University
> 357 Chemistry
> Detroit, MI 48201
> Lab Phone 313-577-0552
> Cell Phone 906-235-0768

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