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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.<br>
<br>
Tom<br>
<br>
<br>
<blockquote
cite="mid:CA++2yUgZM0ZFhkToccNgvDT=jF1CGBsj==vTWdtC_8yPy6f=wg@mail.gmail.com"
type="cite">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"><<a moz-do-not-send="true"
href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb">
<div class="h5"><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>
<br>
</blockquote>
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