Angle between domains

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Type Python Module
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).


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


  • 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}


# import the "angle_between_domains" command

# 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