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

Tom Goddard goddard at sonic.net
Mon May 14 11:29:47 PDT 2012

Here is the Chimera 1.6.1 session file for the image I sent in the 
previous message (1a0m.jpg) in case you want to see what settings were used.


> Hi Sumitro,
>   I made an image in the style of your image (1a0m.jpg below) using 
> Chimera 1.6.1 and I think it captures the effect of your Chimera 1.5 
> image (ep.png) very well.  The difference is that in your image where 
> the ribbon crosses itself you can sometimes see through the top 
> ribbon.  Actually the top ribbon is only transparent in your image in 
> about half of the crossings due to a Chimera 1.5 ribbon transparency 
> bug.  In the Chimera 1.6.1 image the ribbon is fully opaque so you do 
> not see through it at places where it crosses itself.  I think this 
> produces a better image with less visual depth confusion.  Also I 
> think adding silhouette edges as I did in 1a0m_edges.jpg below 
> improves the perception of ribbon crossovers further.  I think the 
> main virtue of your image is that the ribbon that is further back is 
> lighter in color so it draws less attention.  That is achieved by 
> depth cueing which is the same in Chimera 1.6 and 1.5.  My image 
> perhaps does not illustrate depth cueing as well as yours since I used 
> a different PDB model (didn't have yours) and in my view it doesn't 
> vary as much in depth.
>     Tom
> -------- Original Message --------
> Subject: 	Re: [Chimera-users] semi-transparent ribbon behind 
> semi-transparent surface
> Date: 	Sun, 13 May 2012 18:19:39 +0800
> From: 	Sumitro Harjanto
> To: 	Tom Goddard
> Hi Tom, I've attached an image, it's something like this, can you view 
> it? thanks!
> cheers,
> Sumitro
> On 12 May 2012 00:58, Tom Goddardwrote:
>     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 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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