Difference between revisions of "AngleBetweenHelices"

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{{Infobox script-repo
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|type      = Python Module
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|filename  = anglebetweenhelices.py
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|author    = [[User:Speleo3|Thomas Holder]]
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|license  = BSD
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}}
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{{Infobox psico
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|module    =  psico.orientation
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}}
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<gallery perrow=1 heights=191px widths=250px style="float:right; clear: right">
 
Image:Helix_orientation1.png|Orientation of a helix
 
Image:Helix_orientation1.png|Orientation of a helix
 
Image:Helix_orientation2.png|Orientation of two helices, their angle that separates the two is 145.08 degrees as reported by the script
 
Image:Helix_orientation2.png|Orientation of two helices, their angle that separates the two is 145.08 degrees as reported by the script
 
</gallery>
 
</gallery>
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Calculate angle between alpha-helices or beta-sheets.
 
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.
 
There are four different methods implemented to fit a helix, two of them also work for sheets or loops.
  
 
= Commands =
 
= Commands =
<source lang="python">
 
helix_orientation selection [, visualize [, sigma_cutoff [, quiet ]]]
 
  
helix_orientation_hbond selection [, visualize [, cutoff [, quiet ]]]
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angle_between_helices selection1, selection2 [, method [, visualize ]]
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helix_orientation selection [, visualize [, sigma_cutoff ]]
  
loop_orientation selection [, visualize [, quiet ]]
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helix_orientation_hbond selection [, visualize [, cutoff ]]
  
cafit_orientation selection [, visualize [, quiet ]]
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loop_orientation selection [, visualize ]
  
angle_between_helices selection1, selection2 [, method [, visualize [, quiet ]]]
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cafit_orientation selection [, visualize ]
</source>
 
  
 
= Example =
 
= Example =
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</syntaxhighlight>
 
</syntaxhighlight>
  
== Python Code ==
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== See Also ==
  
{{Template:PymolScriptRepoDownload|anglebetweenhelices.py}}
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* [[angle_between_domains]]
  
[[Category:Plugins]]
 
 
[[Category:Structural_Biology_Scripts]]
 
[[Category:Structural_Biology_Scripts]]
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[[Category:Pymol-script-repo]]

Latest revision as of 09:38, 15 December 2016

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
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.

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

See Also