Howdy everyone, I love this program! Anyway I'm trying to make some figures with distance dashes included. I can obviously change the line thickness (pseudobond display options) in the program, but when I save a high resolution image (no pov ray) the line thickness in has no effect. What to do? Thanks for your help. Drew Waight Stroud Lab Genentech Hall S414
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
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
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
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 -------- 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
Hi Drew, Thanks for your kind words! Now I hope you won't change your mind... The linewidth as shown in the Chimera window is maintained in a final image, but up to a limit. That is, graphics drivers can only render the line up to a certain fatness. When you save a high-res image (more pixels than shown in the Chimera window), especially with supersampling (which makes the initial image NxN times larger than the final image), what you get in the final image may be proportionally thinner than in the Chimera window. The image dialog will report (near the bottom) the maximum attainable linewidth in the final image given the requested image dimensions and the supersampling level. Decreasing the supersampling level and/or image dimensions will increase the attainable line fatness. Generally supersampling is nice because it smooths edges (pixel stairsteps less visible), so I would first see if 2x2 supersampling ameliorates the problem before turning it off entirely. I've run into this problem when making images for a paper, and solved it by using the minimum resolution suggested in the author instructions (I forget, 300 or 600 dpi and image no larger than the columns in that journal) with 2x2 supersampling. For further discussion/explanation, see this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-December/004642.html> A few additional points: (a) make sure you are using a reasonably new version of Chimera, say 1.6.2, because some older versions didn't fatten the lines to compensate for supersampling (b) you can make the pseudobonds into sticks instead of lines -- sticks are not subject to this linewidth issue and can be as fat as you like, but not dotted or dashed. Details in this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-August/007863.html> (c) you could use cylinder or sphere objects to fake a solid dotted or dashed line, but it would be tedious because you would have to figure out the coordinates of each cylinder or sphere yourself (we haven't put anything in Chimera to do it automatically). See this previous post and command "shape" for creating such objects: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-August/007868.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html>> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 7, 2012, at 3:06 PM, Andrew Waight wrote:
Howdy everyone, I love this program! Anyway I'm trying to make some figures with distance dashes included. I can obviously change the line thickness (pseudobond display options) in the program, but when I save a high resolution image (no pov ray) the line thickness in has no effect. What to do? Thanks for your help. Drew Waight Stroud Lab
participants (5)
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Andrew Waight -
Elaine Meng -
Greg Couch -
Rebecca Swett -
Tom Goddard