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Type Python Module
Author(s) Thomas Holder
License BSD
This code has been put under version control in the project Pymol-script-repo

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

Module psico.orientation

Calculate angle between alpha-helices or beta-sheets. There are four different methods implemented to fit a helix, two of them also work for sheets or loops.


angle_between_helices selection1, selection2 [, method [, visualize ]]
helix_orientation selection [, visualize [, sigma_cutoff ]]
helix_orientation_hbond selection [, visualize [, cutoff ]]
loop_orientation selection [, visualize ]
cafit_orientation selection [, visualize ]


import anglebetweenhelices

fetch 2x19, async=0
select hel1, /2x19//B/23-36/
select hel2, /2x19//B/40-54/
# just calculate/visualize orientation of single alpha-helix
helix_orientation_hbond hel1
# get angle between two helices
angle_between_helices hel1, hel2
angle_between_helices hel1, hel2, method=1
angle_between_helices hel1, hel2, method=2
# get angle between beta-sheets
select sheet1, A/47-54/
select sheet6, A/146-149/
angle_between_helices sheet1, sheet6, method=loop_orientation
angle_between_helices sheet1, sheet6, method=cafit_orientation


PyMOL>angle_between_helices hel1, hel2, method=cafit_orientation
Using method: cafit_orientation
Angle: 145.08 deg

See Also