[Chimera-users] semi-transparent ribbon behind semi-transparent surface

[Tom Goddard]

Hi Sumitro,

   It is hard to completely understand your problem without seeing an 
example image made with Chimera 1.5 using the technique you described.  
If you provide such an image we might have suggestions about how to make 
something very similar in the latest Chimera.  The image link you send 
before gives permission denied.

     Tom


> Hi Elaine,
>
> thanks for the reply. I believe you exactly described what I did with 
> this paragraph:
> "In Chimera 1.5  each surface could have its own single-layer 
> transparency.  Thus you could still have multiple transparent layers 
> overall, but only the top layer of each surface.  I'm guessing the 
> image is something like that (I don't have permission to view it)."
> Sadly, I resorted to re-installing CHIMERA 1.5 cos even if I use 
> pastel colours in Chimera 1.6, the effects were far from what I've got 
> using the multiple-single layer transparency previously. Is there any 
> plan to make the transparency setting more customisable in the future? 
> that will be of great help! thanks!
>
> Cheers,
> Sum
>
> On 4 May 2012 00:18, Elaine Meng <meng at cgl.ucsf.edu 
> <mailto:meng at cgl.ucsf.edu>> wrote:
>
>
>     On May 3, 2012, at 8:05 AM, Sumitro Harjanto wrote:
>
>     > Hi Elaine,
>     > I used to use CHIMERA 1.5 to generate some molecular images. and
>     I was able to show a "hint of shadow" of ribbon behind a
>     semitransparent molecular surface. but I realised that I can no
>     longer do that from Chimera 1.6 onwards. I have tried fiddling
>     with the new "single layer transparency" value, but either option
>     did not provide me with the visual effect that I could previously
>     get in chimera 1.5. when I turned off the single layer
>     transparency, the molecular surface became very messy with
>     multiple shades and the color is visibly darker. but If I leave it
>     on, the semi-transparent ribbon was not displayed at all. is there
>     anyway that I can achieve a similar effect in Chimera 1.6? i.e if
>     you're wondering what effect I am talking about here is an
>     example:
>     http://onlinelibrary.wiley.com/store/10.1002/emmm.201200213/asset/image_n/nfig004.jpg?v=1&t=h1rxtmm2&s=152573d22f1245472bbcb8ef11b0fcc757548517
>     <http://onlinelibrary.wiley.com/store/10.1002/emmm.201200213/asset/image_n/nfig004.jpg?v=1&t=h1rxtmm2&s=152573d22f1245472bbcb8ef11b0fcc757548517>
>     > Thanks, Elaine!
>     > Cheers,
>     > Sumitro
>
>     Hi Sumitro!
>     In Chimera 1.5  each surface could have its own single-layer
>     transparency.  Thus you could still have multiple transparent
>     layers overall, but only the top layer of each surface.  I'm
>     guessing the image is something like that (I don't have permission
>     to view it).
>
>     In Chimera 1.6 the choices are only either a single layer of
>     transparency, or all transparent layers.
>
>     In Chimera 1.5 if you turn off single-layer transparency for each
>     surface, the result is the same as in Chimera 1.6 if you turn off
>     global single-layer transparency.  However, I realize that does
>     not help, since you don't want to show all layers (it's often
>     ugly, as you describe).
>
>     I don't know if there is any way to get exactly what you had
>     before, but in 1.6 I suggest trying this:  use single-layer
>     transparency (which is the default), make only the surface
>     transparent, keep the ribbon opaque.  If you want the ribbon to be
>     less bold, try making it a pastel color.
>
>     I am not involved in the graphics programming -- I CC'd the list
>     since the other developers may have suggestions (and other users
>     might find the discussion informative).
>     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
>
>
>
>
>
>
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