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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users