Hi, I would like labels to appear bigger like with a bold font. How is that possible? Best JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-users-request@cgl.ucsf.edu Data: Dimecres, Octubre 10, 2012 9:00 pm Assumpte: Chimera-users Digest, Vol 114, Issue 11

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Today's Topics:

1. Re: Coloring nucleic acid ladder with opacity. Possible bug? (Tom Goddard)

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Message: 1 Date: Wed, 10 Oct 2012 10:04:13 -0700 From: Tom Goddard <goddard@sonic.net> To: Rebecca Swett <rswett@chem.wayne.edu> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Coloring nucleic acid ladder with opacity. Possible bug? Message-ID: <5075AA8D.5050304@sonic.net> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

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.

Tom

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Hi Rebecca,

Transparency does not work well with Chimera's nucleotide representations (slabs, ladder). Here's a technical explanation

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may help you understand why you see what you see. The

-------- 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 that transparent

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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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End of Chimera-users Digest, Vol 114, Issue 11 **********************************************