[Chimera-users] layering problem

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 16 10:52:09 PDT 2014

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


… 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 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 at 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
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