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<div class="moz-cite-prefix">Hi Tom,<br>
<br>
that's great! and bisectioning is the way to go :)<br>
<br>
Best,<br>
Martin<br>
<br>
<br>
On 25.11.2013 22:03, Tom Goddard wrote:<br>
</div>
<blockquote
cite="mid:3AA1B579-D0C8-4D93-A68B-C60BC03D9942@sonic.net"
type="cite">
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Hi Martin,
<div><br>
</div>
<div> Thanks for the script. This is something others have
requested. So I added it to Chimera today, in tonight's daily
builds. </div>
<div><br>
</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>volume #0 encloseVolume
150000<br>
<br>
Uses bisection of the density value until the enclosed volume
differs from the target volume by less than 1e-5 of the target
volume. Uses at most 30 bisection steps. Can set the level for
multiple maps at once</div>
<div>
<div><br>
</div>
<div><span class="Apple-tab-span" style="white-space: pre; "> </span>volume
#0-5 encl 250000</div>
</div>
<div><br>
</div>
<div>Can specify multiple volume values to get multiple surfaces,
for example<br>
<br>
<span class="Apple-tab-span" style="white-space:pre"> </span>volume #0 enclose
150000,300000</div>
<div><br>
</div>
<div>The enclosed volume is in cubic Angstroms if your map grid
spacing is in Angstroms. You can report the current enclosed
volume with the "measure volume" command</div>
<div><br>
</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>measure
volume #0</div>
<div><br>
</div>
<div>Thanks for figuring out code to do this. I used a slight
variation of what you did.</div>
<div><br>
</div>
<div> Tom</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>
<div>On Nov 23, 2013, at 8:41 AM, Martin Turk wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
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<div class="moz-cite-prefix">Hi,<br>
<br>
added another step for fine tunning and reduced number
of steps, now it works much faster. Maybe there is a
better way of doing the threshold steps. I overshoot up,
down then up again, but it works :)<br>
<br>
Best,<br>
Martin<br>
<br>
<br>
<br>
On 23.11.2013 16:29, Martin Turk wrote:<br>
</div>
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cite="mid:5290C9D0.8030009@lmb.uni-muenchen.de"
type="cite">
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<div class="moz-cite-prefix">Hi Shawn, Tom, Eric,<br>
<br>
thanks a lot for the help and for pointing me in the
right direction. Finally I had some time and I've come
up with a script that adjusts the volume level
threshold from the active model to all opened models.
For one model it's not a problem, but when one wants
to adjust the levels for a series of volumes (for
example after a 3d classification run in relion), it
becomes cumbersome to do so for the ~50 models/run.
Maybe other EM users find it handy, that's why I'd
like to share it.<br>
It took me quite some time to find the right
functions, which do the actual measurement. Got lost
in the OpenModels.h, volume.py, volumedialog.py, and
the gui scripts. The rest was easy :-) Thanks again
for your help!<br>
<br>
Best,<br>
Martin Turk<br>
<br>
Beckmann Lab<br>
LMU Gence Center Munich<br>
<br>
<br>
On 18.11.2013 20:49, Eric Pettersen wrote:<br>
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<blockquote
cite="mid:AC3293D4-296E-4649-AF7C-DD6DD40F862E@cgl.ucsf.edu"
type="cite">
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To supplement Shawn and Tom's answers, obviously it
would be best if everything were documented, but in
the absence of that if there is a command that
implements something similar to what you want to do,
you can chase it down in the code base by:
<div><br>
</div>
<div><span class="Apple-tab-span"
style="white-space:pre"> </span>a) looking at
Midas/__init__.py and see if it's one of the
functions in there (they're arranged approximately
alphabetically by command name), and if it's not in
there…</div>
<div><span class="Apple-tab-span"
style="white-space:pre"> </span>b) grep
share/*/ChimeraExtension.py for the command name to
find which module defines the command. Then look in
that module's ChimeraExtension.py to see what
file/method in the module implements the command.</div>
<div><br>
</div>
<div>--Eric</div>
<div><br>
</div>
<div><span class="Apple-tab-span"
style="white-space:pre"> </span>Eric Pettersen</div>
<div><span class="Apple-tab-span"
style="white-space:pre"> </span>UCSF Computer
Graphics Lab</div>
<div><br>
<div>
<div>On Nov 18, 2013, at 9:06 AM, Shawn Waldon
<<a moz-do-not-send="true"
href="mailto:swaldon@cs.unc.edu">swaldon@cs.unc.edu</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div dir="ltr">Hi Martin,
<div><br>
</div>
<div>I am not aware that there is a python
library reference. If there is, I would
appreciate a pointer to it as well. Here
are a few links I have found helpful when
writing python code for Chimera:</div>
<div><br>
</div>
This shows how to execute command line
commands, it may be what you want:<br class="">
<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/data/downloads/1.8/docs/ProgrammersGuide/basicPrimer.html">http://www.cgl.ucsf.edu/chimera/data/downloads/1.8/docs/ProgrammersGuide/basicPrimer.html</a>
<div> <br>
</div>
<div>This goes through how to make plugins and
such, but is helpful since the examples show
more of the API:<br>
<div><a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html">http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html</a></div>
</div>
<div><br>
</div>
<div>HTH,</div>
<div>Shawn Waldon</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Mon, Nov 18, 2013
at 9:10 AM, Martin Turk <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:turk@lmb.uni-muenchen.de"
target="_blank">turk@lmb.uni-muenchen.de</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">Hi,<br>
<br>
I am trying to write a simple python
script that will iterate over opened
volumes and adjust the contour level to a
certain mass. This shouldn't be more than
~10 lines. However, I can't find chimera's
python library reference to look up the
class structure and operator names.<br>
<br>
Does someone know how, for example, set
volume level to 0.01 would look like in
python?<br>
in the command line it would be for all
models: volume #0-99 level 0.01<br>
<br>
for models I've found chimera.openModels
and then you can list over them, but
that's about it.<br>
<br>
Thanks,<br>
Martin Turk<br>
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</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">Shawn Waldon
<div>Graduate Research Assistant</div>
<div>Department of Computer Science</div>
<div>University of North Carolina at Chapel
Hill</div>
<div><a moz-do-not-send="true"
href="mailto:swaldon@cs.unc.edu"
target="_blank">swaldon@cs.unc.edu</a></div>
</div>
</div>
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</blockquote>
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<span><chimera-volbymass3.py></span></blockquote>
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