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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}
A Random PyMOL-generated Cover. See Covers.