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<p>So, if you have a graphics card, the full version of chimera will
be *much* faster for 3D graphics. So depending on your definition
of efficient, the full version is way more efficient. The
offscreen rendering is done with a software implementation of
OpenGL using OSMesa. And the bundled version of OSMesa is
ancient, so it is believable that some of Chimera's graphics are
not rendered properly.</p>
<p>Possible solutions: (A) use the full version of Chimera, (B)
install the system version of OSMesa and remove
CHIMERA/lib/libOSMesa.so*, so Chimera picks up the system version
(but currently the Ubuntu/CentOS/RHEL versions only support OpenGL
2.1), (C) compile OSMesa from the Mesa source, <a class="moz-txt-link-abbreviated" href="http://www.mesa3d.org">www.mesa3d.org</a>,
needs the --enable-gallium-llvm option for OpenGL 3.3 support, (D)
wait a week and use ChimeraX (I'm debugging the offscreen support,
and it bundles a version of OSMesa that should work for Chimera
too), or (E) extract the libOSMesa.so from ChimeraX and put it in
CHIMERA/lib.</p>
<p>I'd skip solution (C). (D) is recommended if ChimeraX has enough
support for what you need to do -- it is more short term work for
better results. (B) is easy if it works. (E) is more likely to
work than (B). (A) is best for just getting things done quickly.</p>
<p> HTH,</p>
<p> Greg<br>
</p>
<div class="moz-cite-prefix">On 11/16/2018 8:33 PM, Chemmama, Ilan
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:ED727A3B-1877-4ACD-8136-984A5876FCE3@ucsf.edu">
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<div class=""><span style="font-family: ArialMT;" class="">Dear
developers, </span><br style="font-family: ArialMT;" class="">
</div>
<div class=""><span style="font-family: ArialMT;" class=""><br
class="">
</span></div>
<div class=""><span style="font-family: ArialMT;" class="">I am
trying to create a bunch of images using Chimera. </span></div>
<div class=""><span style="font-family: ArialMT;" class="">I wrote
a script that create the scene using the following steps:</span></div>
<div class=""><span style="font-family: ArialMT;" class=""><br
class="">
</span></div>
<div class="">
<div class=""><font class="" face="ArialMT"><b class="">mc_frame=str(INPUT_FRAME_NUMBER)</b></font></div>
<div class=""><font class="" face="ArialMT"><b class="">rmffile=str("PATH_TO_RMF")</b></font></div>
<div class=""><font class="" face="ArialMT"><b class=""><br
class="">
</b></font></div>
<div class=""><font class="" face="ArialMT"><b class="">runCommand('open
'+rmffile)</b></font></div>
<div class=""><font class="" face="ArialMT"><b class=""><br
class="">
</b></font></div>
<div class=""><font class="" face="ArialMT"><b class="">runCommand('set
bgcolor white')</b></font></div>
<div class=""><font class="" face="ArialMT"><b class="">runCommand('windowsize
1028 1028')</b></font></div>
<div class=""><font class="" face="ArialMT"><b class="">runCommand('~set
depthCue')</b></font></div>
<div class=""><font class="" face="ArialMT"><b class="">runCommand('set
projection orthographic')</b></font></div>
<div class=""><font class="" face="ArialMT"><b class=""><br
class="">
</b></font></div>
<div class=""><span style="font-weight: bold; font-family:
ArialMT;" class="">runCommand('wait 2')</span></div>
</div>
<div class=""><font class="" face="ArialMT">
<div style="font-weight: bold;" class="">runCommand('scale
0.75')</div>
<div style="font-weight: bold;" class="">runCommand('copy file
./Image_'+mc_frame+'.png PNG supersample 3 dpi 300')</div>
<div style="font-weight: bold;" class="">runCommand('close
all')</div>
<div style="font-weight: bold;" class="">runCommand('stop
now’)</div>
<div style="font-weight: bold;" class=""><br class="">
</div>
<div class="">While the scrips works in the headless version
using PDB files, I have not been successful when using RMF
files. </div>
<div class="">The images when using the RMF files are just the
background color (red when set to red, blue when set to
blue) without the structure. </div>
<div class="">I tried also to add the display .2 option as in:</div>
<div class=""><b class="">runCommand(‘display #0.2’) </b></div>
<div class="">which corresponds to the RMF beads scene in the
model panel. </div>
<div class=""><br class="">
</div>
<div class="">I should add that using the GUI version of
chimera, the script works fine and all the images are
properly created.</div>
<div class=""><br class="">
</div>
<div class="">Do you have any hints/clues on what could be
done to make it work? </div>
<div class="">(I am running the script the full version of
chimera but the headless should be more efficient). </div>
<div class=""><br class="">
</div>
<div class="">Thanks, </div>
<div class="">Ilan</div>
</font></div>
<br>
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<br>
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</pre>
</blockquote>
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