[Chimera-users] semi-transparent ribbon behind semi-transparent surface
Tom Goddard
goddard at sonic.net
Mon May 14 10:46:12 PDT 2012
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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