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Some of the difficulties in putting APBS into Chimera are: 1) There
are a lot of parameters in an APBS calculation, 2) It can take a lot
of memory when running (I recall 1 Gbyte for a few thousand atom
protein), 3) It can take a long time to compute.<br>
<br>
None of these prevent it from going in to Chimera but to make it
work well requires significant work. Someone would have to decide
which are the most important parameters to allow the user to
change. It might be very helpful to estimate the peak memory usage
for instance when choosing grid spacing since once it exceeds the
physical memory of the machine it will be extremely slow and could
make the machine unusable while it runs. It also should not freeze
Chimera when running since even a modest computation takes minutes I
think.<br>
<br>
Tom<br>
<br>
<br>
<blockquote
cite="mid:F54CDFCD-10AA-4AAF-A383-2706B6DA7F8C@cgl.ucsf.edu"
type="cite">Yeah, there were some tentative feelers about such a
plugin a couple of years back, but it fizzled out. If you made a
request on the APBS-users list (<a moz-do-not-send="true"
href="http://sourceforge.net/mail/?group_id=148472">SourceForge.net:
Mailing Lists for APBS</a>) they might consider it.
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<div>--Eric</div>
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<div style="margin-top: 0px; margin-right: 0px; margin-bottom:
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face="Helvetica" size="5"> Eric
Pettersen</font></div>
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Computer Graphics Lab</font></div>
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</font></div>
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<div>On Jan 6, 2012, at 7:25 AM, Boaz Shaanan wrote:</div>
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<blockquote type="cite">
<div>Hi Elaine,<br>
<br>
Following on the recent exchange of messages: I've
actually been wondering for quite some time why there
isn't an APBS plugin for Chimera. Is it because of no
interest on the APBS side? Should we ask them to develop
one? I'm sure we can collect enough votes to promote
that. For example, I find the Consurf and Castp plugins
(maybe interfaces, whatever they should be called) very
nice and useful, so why not APBS too?<br>
<br>
Happy New Year to you all (still not too late).<br>
<br>
Boaz<br>
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