<html><body><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000"><div>Hi!</div><div><br data-mce-bogus="1"></div><div>I would like to create a function to copy the torsion angle from a model to another one.</div><div>The function would take in argument the model ID of the reference and target model (<int>) and the residue id (<int>).</div><div>I looked a bit at the scripts available in <a href="https://rbvi.github.io/chimerax-recipes/">https://rbvi.github.io/chimerax-recipes/</a> to have an idea of how to add function in ChimeraX, but I'm currently stuck at "how to get the list of atoms from a selection string ?".</div><div><br data-mce-bogus="1"></div><div>Here's my current script </div><div><hr></div><div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;">from chimerax.core.commands import run</span></div><div><br></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> </span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;">def copy_torsion(session, model1, model2, residue):</span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> selection = f"torsion #{model2}:{residue}@n,ca,c:{residue+1}@n"</span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> from chimerax.atomic import AtomsArg</span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> </span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> atoms = AtomsArg(selection) </span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> </span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> from chimerax.geometry import dihedral </span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> cur_torsion = dihedral([*a.scene_coord for a in atoms])</span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> </span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> torsion=run(session, f"torsion #{model1}:{residue}@n,ca,c:{residue+1}@n {cur_torsion}")</span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> </span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> </span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;">def register_command(logger):</span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> from chimerax.core.commands import CmdDesc, register, FloatArg, IntArg, BoolArg, Color8Arg, StringArg</span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> from chimerax.atomic import AtomsArg</span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> desc = CmdDesc(required = [</span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> ('model1', IntArg),</span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> ('model2', IntArg),</span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> ('residue', IntArg),</span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> ],</span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> synopsis='Copy torsion angle')</span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> register('copyTorsion', desc, copy_torsion, logger=logger)</span></div><div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> <!--StartFragment--></span><div style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; text-decoration-thickness: initial; text-decoration-style: initial; text-decoration-color: initial;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; text-decoration-thickness: initial; text-decoration-style: initial; text-decoration-color: initial;"><br></div><div style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; text-decoration-thickness: initial; text-decoration-style: initial; text-decoration-color: initial;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; text-decoration-thickness: initial; text-decoration-style: initial; text-decoration-color: initial;"><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;">register_command(session)</span></div><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"><!--EndFragment--> </span></div><div><hr></div><div>Thank you for your help :)</div><div><br>Best regards,</div><div>Thibault.</div></div><div><br></div><div><br data-mce-bogus="1"></div><div data-marker="__SIG_PRE__"><div>--<br>Thibault Tubiana, PhD</div><div>Postdoctoral Fellow @<a href="https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanisms-of-proteins-and-peptides/" target="_blank">IMAPP</a><br></div><div><div><span style="font-size: 12pt;">Institute for integrative biology of the cell (<a href="https://www.i2bc.paris-saclay.fr" target="_blank">I2BC</a>) - CNRS UMR 9198</span><br></div><div>CEA Saclay, 91191 Gif sur Yvette - Bât 532 pce 34</div><div>Web Site: <a href="http://www.tubiana.me/" target="_blank">http://www.tubiana.me/</a><br></div></div><div><br></div></div></div></body></html>