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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">An additional question:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Is it possible to retrieve the atomic coordinates after a transformation (e.g. after an align/superposition operation) rather than the original coordinate
values?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">e.g. I am currently using the following commands to retrieve the coordinates (x,y,z) of the CA atom in model,residue,chain<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">atom = chimera.selection.OSLSelection("#%d:%d.%c@CA" % (model,residue,chain)).vertices()<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">(x,y,z) = atom[0].coord()<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">However, this retrieves the original coordinates not the coordinates after a transformation.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hernando<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hernando Sosa<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dept. of Physiology and Biophysics
<br>
Albert Einstein College of Medicine <br>
1300 Morris Park Av. <br>
Bronx NY 10461 <br>
phone (718) 430-3456 <br>
FAX (718) 430-8819 <br>
email <a href="mailto:hernando.sosa@einstein.yu.edu">hernando.sosa@einstein.yu.edu</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Chimera-users [mailto:chimera-users-bounces@cgl.ucsf.edu]
<b>On Behalf Of </b>Hernando J Sosa<br>
<b>Sent:</b> Thursday, October 25, 2018 12:50 PM<br>
<b>To:</b> chimera-users BB<br>
<b>Subject:</b> [Chimera-users] python script<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear Chimera,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I am writing a Chimera python script and need to get a list of the chains and residue numbers of specific opened models . What would be the command/syntax
to do that? or can you point me to a code example where something like this is done.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hernando <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Chimera-users [<a href="mailto:chimera-users-bounces@cgl.ucsf.edu">mailto:chimera-users-bounces@cgl.ucsf.edu</a>]
<b>On Behalf Of </b>Hernando J Sosa<br>
<b>Sent:</b> Monday, June 11, 2018 2:46 PM<br>
<b>To:</b> Eric Pettersen<br>
<b>Cc:</b> chimera-users BB<br>
<b>Subject:</b> Re: [Chimera-users] python script<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks Eric,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">These alternatives is what I was looking for.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Best<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hernando<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Eric Pettersen [<a href="mailto:pett@cgl.ucsf.edu">mailto:pett@cgl.ucsf.edu</a>]
<br>
<b>Sent:</b> Friday, June 08, 2018 7:27 PM<br>
<b>To:</b> Hernando J Sosa<br>
<b>Cc:</b> chimera-users BB<br>
<b>Subject:</b> Re: [Chimera-users] python script<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Hernando,<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>Perhaps runCommand should return a value but it doesn’t. The reasoning there was that the argument to runCommand could be anything, including several commands separated by semi-colons, so
in some cases it’s confusing what the return value should be. In any case that ship has sailed and you have to do something else to get the value. In most cases it calling the underlying function that performs the command and using it’s return value, but
looking at the code that implements the “measure center” command I can see that it doesn’t return anything either.<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>So in the particular case of the example you provided, I can see two options for getting the value:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Option 1)<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>atoms = chimera.selection.OSLSelection(“#0:.A@CA”).vertices()<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>center = chimera.Point([a.coord() for a in atoms])<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>x, y, z = center.data()<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Option 2)<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>rc(“sel #0:.A@CA”)<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>center = chimera.Point([a.coord() for a in chimera.selection.currentAtoms()])<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>x, y, z = center.data()<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I hope this helps.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">—Eric<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="color:black">
</span></span><span style="color:black">Eric Pettersen<o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="color:black">
</span></span><span style="color:black">UCSF Computer Graphics Lab<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
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<p class="MsoNormal">On Jun 8, 2018, at 11:10 AM, Hernando J Sosa <<a href="mailto:hernando.sosa@einstein.yu.edu">hernando.sosa@einstein.yu.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear Chimera,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Is it possible to assign the result of running a chimera command in python to a string or something else? E.g doing something like:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">from chimera import runCommand as rc</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">myresult = rc('measure center #0:.A@CA')</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">And then using the myresults somewhere else in the script after parsing for the relevant values?</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Maybe there is a n easier way to accomplish this?</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hernando</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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