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<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 & guide<br />
<br />
== See Also ==<br />
<br />
* [[intra_xfit]]<br />
* [[align]]<br />
<br />
[[Category:Script Library]]<br />
[[Category:Structural_Biology_Scripts]]</div>
Speleo3