<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Ben,<div class=""><br class=""></div><div class=""> It is very likely that you are reading the 80S ribosome structure in mmcif format. You may not even be aware of this because if you use the command "open 3abc" and the PDB format file is not available because it is a newly deposited structure with more thatn 100,000 atoms or more than 62 chains, the Chimera will automatically fetch the mmCIF version instead (I think this is true for the Chimera daily build). At any rate, the Chimera mmCIF reader is phenomenally slow and takes extreme amounts of memory. It is all written in Python by another lab so we are not familiar with the code. To speed this up you have to read PDB format files instead. You can download the PDB format files from the PDB web site even for new large structures as a tar gzip archive. The big structures will be in multiple files PDB format files.</div><div class=""><br class=""></div><div class=""> As Greg said, our next generation ChimeraX will read large mmCIF files very fast, faster than the current Chimera reads PDB format, but ChimeraX is not yet released.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Mar 17, 2016, at 12:23 PM, Greg Couch wrote:</div><br class="Apple-interchange-newline"><div class="">
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Please use Chimera's Help / Report a Bug dialog to file this as a
bug, and, if possible, give the PDB id of the 80S ribosome you are
trying to view. That will tell us about your computer and the size
of the structure you're trying to view, and that will enable us to
give a better answer.<br class="">
<br class="">
So, my guess it that you are trying view a structure that is too big
for your computer to handle quickly. So the solution would be to
increase the physical memory. You may also need a graphics card
with more memory. Another possibility is that you are reading in
the structure using the mmCIF reader -- in Chimera, the mmCIF reader
is slow and the solution is to use the PDB format version. Our
Chimera successor, ChimeraX, reads mmCIF files very quickly and can
handle large files with ease. Unfortunately, ChimeraX is not yet
available.<br class="">
<br class="">
HTH,<br class="">
<br class="">
Greg<br class="">
<br class="">
<div class="moz-cite-prefix">On 03/17/2016 03:15 AM,
wrote:<br class="">
</div>
<blockquote cite="mid:CFBD0B66-A079-4CFE-AA58-D7A9191DD3C7@ana.unibe.ch" type="cite" class="">
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<div class="">
<div class="">Hello </div>
<div class="">Opening a model of the 80S ribosome takes about 30
minutes on my computer (chimera version 1.10.2 build
40686). Is it normal? Is there any way to speed up this
step (for example, can the task be parallelized)? </div>
<div class="">Thanks in advance</div>
<div class="">Ben</div>
</div>
<div class="">
<div id="MAC_OUTLOOK_SIGNATURE" class="">
<div class="">
<div class="">-- </div>
<div class="">Prof. Benoît Zuber</div>
</div>
<div class="">Institute of Anatomy</div>
<div class="">University of Bern</div>
<div class="">Baltzerstrasse 2</div>
<div class="">Postfach 922</div>
<div class="">3000 Bern 9</div>
<div class="">Switzerland</div>
<div class=""><a class="moz-txt-link-abbreviated" href="mailto:benoit.zuber@ana.unibe.ch">benoit.zuber@ana.unibe.ch</a></div>
<div class="">+41 31 631 84 40</div>
<div class=""><a class="moz-txt-link-freetext" href="http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html">http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html</a></div>
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