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<div>Thank you Tom. </div>
<div>I appreciate it,</div>
<div>Shubham.</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> August 2, 2022 4:15 PM<br>
<b>To:</b> Shubham Devesh Ramgoolam <sdramgoolam@uwaterloo.ca><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Time-efficient python code for obtaining coordinates of atoms</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Shubham,
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<div class=""> Here is example Python code to lookup residues by chain identifier and residue numbers.</div>
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span><a href="https://rbvi.github.io/chimerax-recipes/residues/residues.html" class="">https://rbvi.github.io/chimerax-recipes/residues/residues.html</a></div>
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<div class=""> Tom</div>
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<div class="">On Aug 1, 2022, at 10:39 PM, Shubham Devesh Ramgoolam via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
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Ok. Thank you, Eric.</div>
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I appreciate it,</div>
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Shubham</div>
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Sent from<span class="x_Apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986" class="" style="color:blue; text-decoration:underline">Mail</a><span class="x_Apple-converted-space"> </span>for Windows</div>
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<b class="">From:<span class="x_Apple-converted-space"> </span></b><a href="mailto:pett@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">Eric Pettersen</a><br class="">
<b class="">Sent:<span class="x_Apple-converted-space"> </span></b>Tuesday, August 2, 2022 5:34<br class="">
<b class="">To:<span class="x_Apple-converted-space"> </span></b><a href="mailto:sdramgoolam@uwaterloo.ca" class="" style="color:blue; text-decoration:underline">Shubham Devesh Ramgoolam</a><br class="">
<b class="">Cc:<span class="x_Apple-converted-space"> </span></b><a href="mailto:chimerax-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">chimerax-users@cgl.ucsf.edu</a><br class="">
<b class="">Subject:<span class="x_Apple-converted-space"> </span></b>Re: [chimerax-users] Time-efficient python code for obtaining coordinates of atoms</div>
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Hi Shubham,</div>
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First off, 'getcrd' really should return the coordinates in addition to logging them, so I have fixed that and the fix will be in tonight's daily build.</div>
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But I don't think that really helps you because atom-spec parsing in ChimeraX is relatively slow, and I assume you would need to provide the same (long) atom spec to getcrd that you were using with "sel". We want to improve the speed and reliability of atom-spec
parsing, but achieving that is quite aways off at this point and so won't help with your current situation.</div>
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I assume that which residues you need coordinates from are changing frequently, otherwise the cost of selecting them once wouldn't be that big a deal. Depending on what criteria you are using to choose the residues, maybe you could loop through chimerax.atomic.all_structures(session).residues
and get the coordinates of the residues that meet your criteria.</div>
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--Eric</div>
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Eric Pettersen</div>
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UCSF Computer Graphics Lab</div>
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On Aug 1, 2022, at 2:32 AM, Shubham Devesh Ramgoolam via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
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Hi all,</div>
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I hope you are doing well.</div>
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I am looking for a time-efficient way of obtaining the coordinates of specified residues.</div>
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I cannot use the command getcrd as I need these coordinates in a python script for defining geometric objects (getcrd prints the output to the log).</div>
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My attempt at this consisted of selecting all of the specified residues via run(session, ‘sel ...’), accessing that selection using selected_residues(session), and then, extracting the coordinates using .atoms.coords.</div>
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The issue here is that run(session, ‘sel ...’) slows down if there are lots of specified residues.</div>
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I tried bypassing the command ‘sel’ by first importing AtomSpecArg from chimerax.core.commands.atomspec and then using AtomSpecArg.parse('my residue_ID', session)[0].evaluate(session).atoms[0]. However, this is even slower.</div>
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Regards,</div>
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Shubham</div>
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Sent from<span class="x_apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986" class="" style="color:blue; text-decoration:underline">Mail</a><span class="x_apple-converted-space"> </span>for Windows</div>
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