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Hi Julio<br>
<br>
The Chimera fitting code does a full 3-degree-of-freedom rotational
search. It cannot search fewer rotational degrees of freedom. It
would be nice to adapt the code to be able to consider only rotations
about an axis. The needed changes would be in the FitMap Chimera
module not the fitnogui.py script. Optimizing using only two
rotational degrees of freedom that are Euler angles seems like a
bizarre case and we are not likely to ever handle that.<br>
<br>
Please post future questions to the chimera-users mailing list so
others can answer and read the answers.<br>
<br>
Tom<br>
<br>
<blockquote cite="mid:411A4F29-4156-4845-B914-68EA2BC5078A@uth.tmc.edu"
type="cite">Hi Tom,
<div><br>
</div>
<div>Sorry to bother you again. Is there a way fix one of the Euler
angles for the fitting? Since we have a small theta, we would like to
fix psi=0, and optimize on phi and theta only, plus the translations.
I'm using the fitnogui script.</div>
<div><br>
</div>
<div>Many thanks,</div>
<div>Julio</div>
<div><br>
</div>
<div><br>
<div>
<div>On Jul 28, 2010, at 5:13 PM, Tom Goddard wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div><br>
Hi Julio,<br>
<br>
I guess you are using the fitnogui.py script.<br>
<br>
<br>
<a moz-do-not-send="true"
href="http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/fitnogui.py">http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/fitnogui.py</a><br>
<br>
The parameters are right near the top -- ijk_step_size_min is the one <br>
you're interested in.<br>
<br>
The initial contour level is set as described in the documentation:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#dispsurf">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#dispsurf</a><br>
<br>
The "volume" command can set the contour level:<br>
<br>
volume #0 level 27.6<br>
<br>
Tom<br>
<br>
<blockquote type="cite">Hi Tom,<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Thanks again. Editing the line of code
would be perfect for us, since we are calling Chimera from our program
with the "nogui" option. Could you point me the place where I need to
change that 0.01?<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">What happens with the contour level when
I'm calling Chimera in that way (nogui)? Can I similarly set it
somewhere in the code? Or with an option in the command line?<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Best,<br>
</blockquote>
<blockquote type="cite">Julio<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><font class="Apple-style-span"
color="#000000"><font class="Apple-style-span" color="#006312"><br>
</font></font></blockquote>
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</blockquote>
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</blockquote>
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