[Chimera-users] Stereo Red Cyan
amcdonald at boisestate.edu
Thu Sep 24 06:53:26 PDT 2020
Red Cyan stereo is working with transparent solid in the 09/23/2020 build.
Thank you all.
On Tue, Sep 22, 2020 at 7:02 PM Tom Goddard <goddard at sonic.net> wrote:
> Hi Michael, Angus, Elaine,
> The solid style volume rendering does only show red and gray with no
> cyan and that is a bug. I also see that surface style works correctly if
> the surface is opaque, but if the surface is even the slighting bit
> transparent (0.99 opaque) then cyan disappears. The solid style is also a
> form of transparent rendering. I believe that all transparent models will
> fail to show the cyan and so anaglyph stereo will not work with
> transparency. This bug is likely related to the fact that Chimera cannot
> correctly combine two transparent models.
> We currently only fix critical bugs in Chimera since all development
> effort and funding is for the next generation ChimeraX (which does not yet
> have anaglyph stereo). I've made a ticket for this Chimera bug
> but we do not have the resources to fix it.
> On Sep 22, 2020, at 5:09 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hello Angus and Michael,
> It may be a function of the map display style. If I open a map from EMDB,
> e.g. commands:
> open emdbID:1024
> stereo anaglyph
> I can clearly see the 3D effect when wearing red-cyan glasses (and red and
> cyan fringes with the glasses taken off) if I am showing surface or mesh
> isosurfaces for the map, but not if showing the diffuse cloud of the
> "solid" style. I attach an image of the map in surface style.
> I don't know if you can expect to see a 3D effect with the transparent
> "solid" style even with anaglyph stereo working correctly. I couldn't
> perceive it with that style.
> Tested Chimera 1.14 on Mac, and I believe that the map from EMDB is 32-bit
> floating point like your data.
> I hope this helps,
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Sep 22, 2020, at 10:03 AM, Greg Couch <gregc at cgl.ucsf.edu> wrote:
> Yes, the red and gray is normal, but you're seeing the combined channels.
> You need the glasses to separate the channels. Try viewing the image with
> the glasses that come with a 3D comic book.
> -- Greg
> On 9/21/2020 11:43 PM, Michael Elbaum wrote:
> Red-cyan, sorry. No, I didn't look for stereo at all, just to reproduce
> the condition posted that one channel appears in red and the other in gray.
> Is that normal?
> From: Greg Couch <gregc at cgl.ucsf.edu>
> Sent: Tuesday, September 22, 2020 4:57:50 AM
> To: Michael Elbaum <michael.elbaum at weizmann.ac.il>
> Subject: Re: [Chimera-users] Stereo Red Cyan
> Are you wearing red-cyan glasses to see the stereo? It doesn't work
> without them.
> -- Greg
> On 9/21/2020 1:08 PM, Michael Elbaum wrote:
> I'm confirming the problem with a different dataset (optical deconvolution
> in tif format). Red-green shows red and gray, green-magenta shows green and
> gray. This is with version 1.14 on linux.
> From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of
> Angus McDonald <amcdonald at boisestate.edu>
> Sent: Monday, September 21, 2020 9:46:24 PM
> To: chimera-users at cgl.ucsf.edu BB
> Subject: [Chimera-users] Stereo Red Cyan
> I am looking at some cryo em data. When I try to view a a 3D stack of em
> dat with the Red-Cyan stereo setting I seem to only get Red and grayscale.
> The data is in 32-bit floating point and is in MRC2014 header format. I
> cannot figure out what I am doing wrong. Is anything obvious?
> Thanks for your time.
> Angus McDonald
> amcdonald at boisestate.edu
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amcdonald at boisestate.edu
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