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|author = [[User:Speleo3|Thomas Holder]] | |author = [[User:Speleo3|Thomas Holder]] | ||
|license = BSD | |license = BSD | ||
+ | }} | ||
+ | |||
+ | {{Infobox psico | ||
+ | |module = psico.orientation | ||
}} | }} | ||
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= Commands = | = Commands = | ||
− | |||
− | |||
− | + | 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 ] | |
− | |||
= Example = | = Example = | ||
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Angle: 145.08 deg | Angle: 145.08 deg | ||
</syntaxhighlight> | </syntaxhighlight> | ||
+ | |||
+ | == See Also == | ||
+ | |||
+ | * [[angle_between_domains]] | ||
[[Category:Structural_Biology_Scripts]] | [[Category:Structural_Biology_Scripts]] | ||
[[Category:Pymol-script-repo]] | [[Category:Pymol-script-repo]] |
Latest revision as of 05:54, 9 January 2017
Type | Python Module |
---|---|
Download | anglebetweenhelices.py |
Author(s) | Thomas Holder |
License | BSD |
This code has been put under version control in the project Pymol-script-repo |
Included in psico | |
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.
Commands
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 ]
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