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

Module psico.fitting

xfit does a weighted superposition of two structures. The weights are estimated with maximum likelihood.

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).


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


xfit mobile, target [, mobile_state [, target_state [, load_b
    [, cycles [, match [, guide [, seed ]]]]]]]


  • mobile = string: atom selection
  • target = string: atom selection
  • mobile_state = int: object state of mobile selection {default: current}
  • target_state = int: object state of target selection {default: current}
  • load_b = 0 or 1: save -log(weights) into B-factor column {default: 0}
  • cycles = int: number of weight refinement cycles {default: 10}
  • match = align or super: alignment method {default: align}
  • 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 4akeA 1akeA, async=0

xfit 4akeA, 1akeA, load_b=1

spectrum b, blue_white_red, 4akeA & guide

See Also