layering problem
Hi!
I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this?
Cheers, Joe
Hi Joe,
Chimera shows one transparent layer by default. If two transparent objects are on top of each other than the transparent part behind is not shown. Chimera can show multiple transparent layers (menu Tools / View Controls / Effects, turn of “single-layer” transparency). But this isn’t going to help you because Chimera does not correctly display two or more superimposed transparent models. The transparent model behind will sometimes appear to be in front. This limitation is because Chimera draws one model at a time in a specific order, and multiple transparent models can’t be handled by this graphics rendering method.
Why are you trying to make the atoms transparent? The only good use of this I have seen is to fade in/out atoms. A better way to do that is to use the “movie crossfade” command which smoothly interpolates from one image to the next. The limitation of that technique is that you cannot have motion at the same time as the fade in / out.
Tom
On Jul 16, 2014, at 2:13 AM, Joseph Atherton j.atherton@mail.cryst.bbk.ac.uk wrote:
Hi!
I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this?
Cheers, Joe <morph_kin3_ADP_release_trial.mp4>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks Tom, that worked well. Just trying to demonstrate a part of the model which has high flexibility until a structural change, and the faded atoms seem to work decently!
Cheers, Joe
On 16/07/2014 18:50, Tom Goddard wrote:
Hi Joe,
Chimera shows one transparent layer by default. If two transparent objects are on top of each other than the transparent part behind is not shown. Chimera can show multiple transparent layers (menu Tools / View Controls / Effects, turn of “single-layer” transparency). But this isn’t going to help you because Chimera does not correctly display two or more superimposed transparent models. The transparent model behind will sometimes appear to be in front. This limitation is because Chimera draws one model at a time in a specific order, and multiple transparent models can’t be handled by this graphics rendering method.
Why are you trying to make the atoms transparent? The only good use of this I have seen is to fade in/out atoms. A better way to do that is to use the “movie crossfade” command which smoothly interpolates from one image to the next. The limitation of that technique is that you cannot have motion at the same time as the fade in / out.
Tom
On Jul 16, 2014, at 2:13 AM, Joseph Atherton j.atherton@mail.cryst.bbk.ac.uk wrote:
Hi!
I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this?
Cheers, Joe <morph_kin3_ADP_release_trial.mp4>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Joseph, Yes, there is a “single-layer” transparency setting (on by default) to show only the topmost of multiple transparent layers. You can control it in the Effects tool or with a command, e.g.
~set singlelayer
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#singlelayer
… to turn it off. Note multiple transparent layers can add visual complexity and make a structure harder to understand, and sometimes Chimera has problems in rendering them correctly. That’s not to say you might not want them sometimes, just be aware of the potential issues! 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 Jul 16, 2014, at 2:13 AM, Joseph Atherton j.atherton@mail.cryst.bbk.ac.uk wrote:
Hi!
I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this?
Cheers, Joe <morph_kin3_ADP_release_trial.mp4>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
One idea is to show the surface as mesh with nontransparent mesh lines, saving transparency for the fading atoms. You could experiment with the surface smoothing and fineness of the mesh. However, I don’t know if that would end up looking good enough for your purposes.
Somewhat as an aside, I recently made a kinase morph movie in which the ATP analog fades (very quickly) but I didn’t have other transparent things in the scene. It’s currently the top entry in our Animation Gallery: http://www.rbvi.ucsf.edu/chimera/animations/animations.html
Elaine
On Jul 16, 2014, at 2:13 AM, Joseph Atherton j.atherton@mail.cryst.bbk.ac.uk wrote:
Hi!
I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this?
Cheers, Joe <morph_kin3_ADP_release_trial.mp4>_______________________________________________
Cheers,
Thanks all!
Joe
On 16/07/2014 19:09, Elaine Meng wrote:
One idea is to show the surface as mesh with nontransparent mesh lines, saving transparency for the fading atoms. You could experiment with the surface smoothing and fineness of the mesh. However, I don’t know if that would end up looking good enough for your purposes.
Somewhat as an aside, I recently made a kinase morph movie in which the ATP analog fades (very quickly) but I didn’t have other transparent things in the scene. It’s currently the top entry in our Animation Gallery: http://www.rbvi.ucsf.edu/chimera/animations/animations.html
Elaine
On Jul 16, 2014, at 2:13 AM, Joseph Atherton j.atherton@mail.cryst.bbk.ac.uk wrote:
Hi!
I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this?
Cheers, Joe <morph_kin3_ADP_release_trial.mp4>_______________________________________________
Hi,
I have a little bug where BLAST searches duplicate each time I save/reopen chimera sessions. Is there any way of closing all blast search windows simultaneously without having to click 'quit' on each one?
Cheers, Joe Atherton
Hi Joe, Re your specific question, sorry no, but the main thing is that it shouldn’t be happening. It would be great if you could use menu: Help… Report a Bug and attach a session that exhibits this problem. Please include a short description and your e-mail address if you want feedback on the bugfix resolution. Thanks, 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 Aug 19, 2015, at 3:14 AM, Joseph Atherton j.atherton@mail.cryst.bbk.ac.uk wrote:
Hi, I have a little bug where BLAST searches duplicate each time I save/reopen chimera sessions. Is there any way of closing all blast search windows simultaneously without having to click 'quit' on each one? Cheers, Joe Atherton
participants (3)
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Elaine Meng -
Joseph Atherton -
Tom Goddard