Xfit
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Included in psico | |
Module | psico.fitting |
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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).
Installation
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
xfit mobile, target [, mobile_state [, target_state [, load_b [, cycles [, match [, guide [, seed ]]]]]]]
Arguments
- 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}
Example
import psico.fitting fetch 4akeA 1akeA, async=0 xfit 4akeA, 1akeA, load_b=1 spectrum b, blue_white_red, 4akeA & guide