Theseus

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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.

Installation

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

Usage

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 ]]]]]

Arguments

  • 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}

Examples

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

intra_theseus 1adz

See Also