[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.
Tom
> 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
>>
>>
>
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120514/8915bf88/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 1a0m.py
Type: text/x-python-script
Size: 73384 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120514/8915bf88/attachment.bin>
More information about the Chimera-users
mailing list