https://wiki.pymol.org/index.php?action=history&feed=atom&title=Xfit 2026-05-08T11:05:43Z Revision history for this page on the wiki MediaWiki 1.35.1 https://wiki.pymol.org/index.php?title=Xfit&diff=14159&oldid=prev 2017-11-13T03:27:09Z

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Cchem https://wiki.pymol.org/index.php?title=Xfit&diff=14158&oldid=prev 2017-10-19T09:20:44Z

<p>created</p> <p><b>New page</b></p><div>{{Infobox psico<br /> |module = psico.fitting<br /> }}<br /> <br /> [[xfit]] does a weighted superposition of two structures. The weights are estimated with maximum likelihood.<br /> <br /> This typically gives better looking superpositions than the [[align]] command, which does simple outlier rejection (equivalent to weight=0 on the rejected atoms, and weight=1 on the included atoms).<br /> <br /> == Installation ==<br /> <br /> [[xfit]] is available from the [[psico]] package and requires [https://github.com/csb-toolbox/CSB CSB].<br /> <br /> 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 speleo3 csb<br /> <br /> == Usage ==<br /> <br /> xfit mobile, target [, mobile_state [, target_state [, load_b<br /> [, cycles [, match [, guide [, seed ]]]]]]]<br /> <br /> == Arguments ==<br /> <br /> * '''mobile''' = string: atom selection<br /> * '''target''' = string: atom selection<br /> * '''mobile_state''' = int: object state of mobile selection {default: current}<br /> * '''target_state''' = int: object state of target selection {default: current}<br /> * '''load_b''' = 0 or 1: save -log(weights) into B-factor column {default: 0}<br /> * '''cycles''' = int: number of weight refinement cycles {default: 10}<br /> * '''match''' = align or super: alignment method {default: align}<br /> * '''guide''' = 0 or 1: use only CA-atoms (protein) or C4' (nucleic acid) {default: 1}<br /> * '''seed''' = 0 or 1: use initial weights from current positions {default: 0}<br /> <br /> == Example ==<br /> <br /> import psico.fitting<br /> fetch 4akeA 1akeA, async=0<br /> <br /> xfit 4akeA, 1akeA, load_b=1<br /> <br /> spectrum b, blue_white_red, 4akeA &amp; guide<br /> <br /> == See Also ==<br /> <br /> * [[intra_xfit]]<br /> * [[align]]<br /> <br /> [[Category:Script Library]]<br /> [[Category:Structural_Biology_Scripts]]</div>

Speleo3