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Wow, thanks a lot to Eric and Elaine for such a useful advice!<br>
Best wishes,<br>
Xavier<br>
<br>
<div class="moz-cite-prefix">On 1/8/14 8:28 PM, Eric Pettersen
wrote:<br>
</div>
<blockquote
cite="mid:0F561D71-C2AD-45AF-8F9D-034ECFF8C5DB@cgl.ucsf.edu"
type="cite">
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Hi Xavier,
<div><span class="Apple-tab-span" style="white-space:pre"> </span>In
addition to Elaine's neon suggestion, if when you save an image
you change the rendering from "Chimera" to "POV-Ray" then any
dashed or dotted lines will be converted into equivalent
cylinders and spheres in the POV-Ray image. I've attached an
image that shows how a distance looks.</div>
<div><br>
</div>
<div>--Eric</div>
<div><br>
<div> Eric Pettersen<br>
UCSF Computer Graphics Lab<br>
<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a><br>
<br>
</div>
<div><img id="08f9086b-cc20-498e-b225-ca9a8ffeb2a2"
apple-width="yes" apple-height="yes"
src="cid:part2.02020304.04010704@ibmb.csic.es" height="762"
width="952"></div>
<br>
<div>
<div>On Aug 1, 2014, at 10:13 AM, Elaine Meng <<a
moz-do-not-send="true" href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">Dear Xavier,<br>
Thanks for your kind words!<br>
<br>
Unfortunately I can’t report any progress in this area. We
did add a “spring” style, but other than manually
calculating coordinates of small spheres and cylinders and
then creating them with command “shape”, my only other idea
for showing dashed lines as 3D objects via Chimera is to use
the “neon” command (not available on Windows). It has many
options and you can even control the lighting, but it is
noninteractive and the parameters are mainly specified by
parameter files neon.dat and conic.dat. It can be quite
labor-intensive (iterative) to get what you want. Also, it
does not include text labels, ribbons, or molecular
surfaces: just spheres, ball-and-stick, sticks, and backbone
“tubes.” I attach an image of the Chimera window and an
image made with the command:<br>
<br>
neon -o neon.tiff -c conic.dat<br>
<br>
with parameter files conic.dat and neon.dat both in the
current Chimera working directory.<br>
<<a moz-do-not-send="true"
href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/neon.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/neon.html</a>><br>
<<a moz-do-not-send="true"
href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/neon1.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/neon1.html</a>><br>
<br>
Sorry I don’t have a better answer,<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>
<span><neon.dat></span><span><conic.dat></span><br>
Chimera window:<br>
<span><chimera.png></span><br>
<br>
neon.tiff using the settings in neon.dat and conic.dat<br>
<span><neon.tiff></span><br>
On Aug 1, 2014, at 6:51 AM, F.Xavier Gomis-Rüth <<a
moz-do-not-send="true" href="mailto:xgrcri@ibmb.csic.es">xgrcri@ibmb.csic.es</a>>
wrote:<br>
<br>
<blockquote type="cite">Dear CHIMERA team,<br>
I moved from SETOR to CHIMERA for preparing nice protein
structure images for publication already some<br>
time ago and am totally happy. Thre is, however, one
single feature that was possible in SETOR but I still miss<br>
in CHIMERA: to draw pseudobonds as dashed sticks or small
spheres. Is it be really not possible to implement<br>
this nuisance? I known Elaine negatively answered a
similar question some time ago within the BB but I would<br>
herewith strike a blow for it again.<br>
Best wishes and thanks for maintaining and devloping such
a fantastic program,<br>
Xavier<br>
-- <br>
<fxgr_signanew.jpg><br>
</blockquote>
<br>
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</blockquote>
</div>
<br>
</div>
<br>
</blockquote>
<br>
<div class="moz-signature">-- <br>
<img src="cid:part8.08040802.09080105@ibmb.csic.es" border="0"></div>
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