[Chimera-users] layering problem

Joseph Atherton j.atherton at mail.cryst.bbk.ac.uk
Thu Jul 17 02:30:15 PDT 2014

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!


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 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>_______________________________________________
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