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Hi Sumitro,<br>
<br>
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.<br>
<br>
Tom<br>
<br>
<br>
-------- Original Message --------
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Subject: </th>
<td>Re: [Chimera-users] semi-transparent ribbon behind
semi-transparent surface</td>
</tr>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Date: </th>
<td>Sun, 13 May 2012 18:19:39 +0800</td>
</tr>
<tr>
<th align="RIGHT" nowrap="nowrap" valign="BASELINE">From: </th>
<td>Sumitro Harjanto <br>
</td>
</tr>
<tr>
<th align="RIGHT" nowrap="nowrap" valign="BASELINE">To: </th>
<td>Tom Goddard</td>
</tr>
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<br>
<br>
Hi Tom, I've attached an image, it's something like this, can you
view it? thanks!
<div><br>
</div>
<div>cheers,</div>
<div>Sumitro<br>
<br>
<div class="gmail_quote">On 12 May 2012 00:58, Tom Goddard<span
dir="ltr"></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> Hi Sumitro,<br>
<br>
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.<span class="HOEnZb"><font
color="#888888"><br>
<br>
Tom<br>
<br>
<br>
</font></span>
<blockquote type="cite">
<div>
<div class="h5">Hi Elaine,
<div><br>
</div>
<div>thanks for the reply. I believe you exactly
described what I did with this paragraph:</div>
"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)."<br>
<div> </div>
<div>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!</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Sum</div>
<div><br>
<div class="gmail_quote">On 4 May 2012 00:18, Elaine
Meng <span dir="ltr"></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0
0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div>
<div><br>
On May 3, 2012, at 8:05 AM, Sumitro Harjanto
wrote:<br>
<br>
> Hi Elaine,<br>
> 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: <a
moz-do-not-send="true"
href="http://onlinelibrary.wiley.com/store/10.1002/emmm.201200213/asset/image_n/nfig004.jpg?v=1&t=h1rxtmm2&s=152573d22f1245472bbcb8ef11b0fcc757548517"
target="_blank">http://onlinelibrary.wiley.com/store/10.1002/emmm.201200213/asset/image_n/nfig004.jpg?v=1&t=h1rxtmm2&s=152573d22f1245472bbcb8ef11b0fcc757548517</a><br>
> Thanks, Elaine!<br>
> Cheers,<br>
> Sumitro<br>
<br>
</div>
</div>
Hi Sumitro!<br>
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).<br>
<br>
In Chimera 1.6 the choices are only either a
single layer of transparency, or all transparent
layers.<br>
<br>
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).<br>
<br>
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.<br>
<br>
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).<br>
I hope this helps,<br>
Elaine<br>
----------<br>
Elaine C. Meng, Ph.D.<br>
UCSF Computer Graphics Lab (Chimera team) and
Babbitt Lab<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
</blockquote>
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