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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.<br>
<br>
Tom<br>
<br>
<br>
<blockquote cite="mid:4FB144E4.7010705@sonic.net" type="cite">
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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 --------
<table class="moz-email-headers-table" border="0" cellpadding="0"
cellspacing="0">
<tbody>
<tr>
<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Subject:
</th>
<td>Re: [Chimera-users] semi-transparent ribbon behind
semi-transparent surface</td>
</tr>
<tr>
<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>
</tbody>
</table>
<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>
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