Intra xfit

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Included in psico
This command or function is available from psico, which is a PyMOL extension.

Module psico.fitting
Intra xfit-1nmr.png

intra_xfit does a weighted superposition of a multi-state object, like an NMR-ensemble. The weights are estimated with maximum likelihood.

This typically gives much better looking ensemble-fittings than the built-in intra_fit command, which does not do any outlier rejection or weighting.

To superpose two different objects, use xfit.


intra_xfit is available from the psico package and requires CSB.

All dependencies are available from Anaconda Cloud:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c speleo3 csb


intra_xfit selection [, load_b [, cycles [, guide [, seed ]]]]


  • selection = string: atom selection from a single multi-state object
  • load_b = 0 or 1: save -log(weights) into B-factor column {default: 0}
  • cycles = int: number of weight refinement cycles {default: 20}
  • guide = 0 or 1: use only CA-atoms (protein) or C4' (nucleic acid) {default: 1}
  • seed = 0 or 1: use initial weights from current positions {default: 0}


import psico.fitting
fetch 1nmr, async=0

intra_xfit 1nmr, load_b=1

spectrum b, blue_white_red, guide

See Also