Angle between domains

Type	Python Module
Download	orientation.py
Author(s)	Thomas Holder
License	BSD-2-Clause

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

angle_between_domains calculates the rotation and displacement that would happen when aligning two atom selections. The typical use case is for two conformations of a multi-domain structure, which is first aligned on domain 1 (e.g. chain A), and then angle_between_domains is calculated for domain 2 (e.g. chain B).

Usage

angle_between_domains selection1, selection2 [, method
    [, state1 [, state2 [, visualize ]]]]

Arguments

• selection1 = str: atom selection in conformation 1
• selection2 = str: atom selection in conformation 2
• method = str: alignment command like "align", "super" or "cealign" {default: align}

Example

# import the "angle_between_domains" command
run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/orientation.py

# two conformations of a two-chain structure
fetch 1ake, s1, async=0
fetch 4ake, s2, async=0

# align on chain A
align s1 & chain A, s2 & chain A

# measure rotation and displacement of chain B
angle_between_domains s1 & chain B, s2 & chain B

For 1ake and 4ake, this reports:

Angle: 15.55 deg, Displacement: 56.08 angstrom

See also

• AngleBetweenHelices
• align, super, cealign
• pymol-users 01 Nov 2012
• pymol-users 13 Jan 2015
• elbow_angle
• RotationAxis