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Hi Eric,<br>
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I can't find the function. Trying to call it within the chimera idle-python shell I get the following error:</div>
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<span>>>> chimera.StructMeasure.axis()<br>
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<div>Traceback (most recent call last):<br>
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<div> File "<pyshell#3>", line 2, in <module><br>
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<span>AttributeError: 'module' object has no attribute 'StructMeasure'</span></div>
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<span>I can't see it either (or something similarly called) within the functions listed if a do</span></div>
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<span>>>>help(chimera)</span></div>
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<span>H.</span><br>
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<div><font size="2" face="Arial"><a><span>___________________________________<br>
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<div><font size="2" face="Arial"><a><span style="font-size:9pt; font-family:Arial,Helvetica,sans-serif">Hernando Sosa</span></a><span><span style="font-size:9pt; font-family:Arial,Helvetica,sans-serif">
</span><span><br>
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<font size="2" face="Arial"><span><span style="font-size:9pt; font-family:Arial,Helvetica,sans-serif">Dept. of Physiology and Biophysics
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<div><font size="2" face="Arial"><span><span></span></span><span><span style="font-size:9pt; font-family:Arial,Helvetica,sans-serif">emai:
</span><span><a href="mailto:hernando.sosa@einsteinmed.org" title="hernando.sosa@einsteinmed.org"><span style="font-size:9pt; font-family:Arial,Helvetica,sans-serif">hernando.sosa@einsteinmed.org</span></a><br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> Friday, July 10, 2020 4:44 PM<br>
<b>To:</b> Hernando J Sosa <hernando.sosa@einsteinmed.org><br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [Chimera-users] axes</font>
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<div>Hi Hernando,
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Mostly yes. The function is chimera.StructMeasure.axis(). There is a doc string for the function describing its arguments and return values. In its simplest form it takes a numpy
array of xyz values and returns a Point (centroid) instance and a Vector (unit direction vector) instance. To get a length you would also have to supply the findBounds=True keyword argument, in which case it will return two additional floating-point values,
the scale factors to apply to the unit vector to get it to the approximate bounds of the axis in each direction (so one of the scale factors will be negative).</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>If you have a list of Atom instances, the easiest way to generate the numpy xyz array is with numpyArrayFromAtoms,
<i class="">e.g.</i><span class="" style="font-style:normal">:</span></div>
<div class=""><br class="">
</div>
<div class="">import chimera</div>
<div class="">xyzs = chimera.numpyArrayForAtoms(atoms)</div>
<div class=""><br class="">
</div>
<div class="">If you only really have an atom spec, let me know and I can help with how to generate a list of Atoms from that.</div>
<div class=""><br class="">
</div>
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<div class="">--Eric</div>
<div class=""><br class="">
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Eric Pettersen</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>UCSF Computer Graphics Lab</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Jul 10, 2020, at 11:54 AM, Hernando J Sosa <<a href="mailto:hernando.sosa@einsteinmed.org" class="">hernando.sosa@einsteinmed.org</a>> wrote:</div>
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Dear Chimera,</div>
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Is there a way to run a command within a python script equivalent to the chimera command 'define axis' to be able to retrieve the results (length,center, direction) ? Something like:</div>
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(length,center,direction) = mydefineaxis(atomspec)</div>
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Thanks</div>
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Hernando<br class="">
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<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">Chimera-users
mailing list:<span class="x_Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">Chimera-users@cgl.ucsf.edu</a><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
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