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

Module psico.fitting

theseus is a wrapper for the theseus program for maximum likelihood superpositioning of macromolecular structures. It produces results very similar to xfit.


For Linux and macOS, all dependencies are available from Anaconda Cloud:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c schrodinger theseus


Superpose two objects:

theseus mobile, target [, match [, cov [, cycles [, mobile_state [, target_state [, exe [, preserve ]]]]]]]

Ensemble-fit states of a multi-state object:

intra_theseus selection [, state [, cov [, cycles [, exe [, preserve ]]]]]


  • mobile = string: atom selection for mobile atoms
  • target = string: atom selection for target atoms
  • match = string: in, like, align, none or the name of an alignment object (see local_rms help for details) {default: align}
  • cov = 0/1: 0 is variance weighting, 1 is covariance weighting (slower) {default: 0}
  • cycles = int: number of weights refinement cycles {default: 200}

For intra_theseus:

  • selection = string: atoms to fit
  • state = integer: keep transformation of this state unchanged {default: 1}


import psico.fitting
fetch 1adz, async=0
set all_states

intra_theseus 1adz

See Also