[Chimera-users] layering problem

[Elaine Meng]

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 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
>> <morph_kin3_ADP_release_trial.mp4>_______________________________________________