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 Goddard wrote:

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
> 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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