AngleBetweenHelices

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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.

Commands

helix_orientation selection [, visualize [, sigma_cutoff [, quiet ]]]

helix_orientation_hbond selection [, visualize [, cutoff [, quiet ]]]

loop_orientation selection [, visualize [, quiet ]]

cafit_orientation selection [, visualize [, quiet ]]

angle_between_helices selection1, selection2 [, method [, visualize [, quiet ]]]

Example

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

Output:

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

Python Code

This code has been put under version control. In the project, Pymol-script-repo.

For a color coded view:

https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/anglebetweenhelices.py

See the raw code or download manually, by right clicking the following link here -> Save as: anglebetweenhelices.py

https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/anglebetweenhelices.py