Intra xfit

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

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.

Installation

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

Usage

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

Arguments

• 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}

Example

import psico.fitting
fetch 1nmr, async=0

intra_xfit 1nmr, load_b=1

spectrum b, blue_white_red, guide

See Also

• xfit
• intra_fit