https://wiki.pymol.org/index.php?action=history&feed=atom&title=Theseus 2026-04-24T10:30:24Z Revision history for this page on the wiki MediaWiki 1.35.1 https://wiki.pymol.org/index.php?title=Theseus&diff=14324&oldid=prev 2018-05-29T19:27:25Z

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Cchem https://wiki.pymol.org/index.php?title=Theseus&diff=14323&oldid=prev 2018-05-15T08:03:25Z

<p>created</p> <p><b>New page</b></p><div>{{Infobox psico<br /> |module = psico.fitting<br /> }}<br /> <br /> [[theseus]] is a wrapper for the [http://www.theseus3d.org/ theseus] program for maximum likelihood superpositioning of macromolecular structures. It produces results very similar to [[xfit]].<br /> <br /> == Installation ==<br /> <br /> For Linux and macOS, all dependencies are available from [https://anaconda.org Anaconda Cloud]:<br /> <br /> conda install -c schrodinger pymol<br /> conda install -c schrodinger pymol-psico<br /> conda install -c schrodinger theseus<br /> <br /> == Usage ==<br /> <br /> Superpose two objects:<br /> <br /> theseus mobile, target [, match [, cov [, cycles [, mobile_state [, target_state [, exe [, preserve ]]]]]]]<br /> <br /> Ensemble-fit states of a multi-state object:<br /> <br /> intra_theseus selection [, state [, cov [, cycles [, exe [, preserve ]]]]]<br /> <br /> == Arguments ==<br /> <br /> * '''mobile''' = string: atom selection for mobile atoms<br /> * '''target''' = string: atom selection for target atoms<br /> * '''match''' = string: in, like, align, none or the name of an alignment object (see [[local_rms]] help for details) {default: align}<br /> * '''cov''' = 0/1: 0 is variance weighting, 1 is covariance weighting (slower) {default: 0}<br /> * '''cycles''' = int: number of weights refinement cycles {default: 200}<br /> <br /> For ''intra_theseus'':<br /> <br /> * '''selection''' = string: atoms to fit<br /> * '''state''' = integer: keep transformation of this state unchanged {default: 1}<br /> <br /> == Examples ==<br /> <br /> &lt;syntaxhighlight lang=&quot;python&quot;&gt;<br /> import psico.fitting<br /> fetch 1adz, async=0<br /> set all_states<br /> <br /> intra_theseus 1adz<br /> &lt;/syntaxhighlight&gt;<br /> <br /> == See Also ==<br /> <br /> * [[xfit]]<br /> * [[intra_xfit]]<br /> * [[intra_fit]]<br /> * [[intra_rms_cur]]<br /> * [[align]]<br /> <br /> [[Category:Structure_Alignment]]<br /> [[Category:Script_Library]]</div>

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