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Difference between revisions of "Elbow angle"

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(removed reference to github example script)
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This script allows you to calculate the elbow angle of an antibody Fab fragment object and optionally draw a graphical representation of the vectors used to calculate the elbow angle.
 
This script allows you to calculate the elbow angle of an antibody Fab fragment object and optionally draw a graphical representation of the vectors used to calculate the elbow angle.
  
=== Examples ===
+
== Examples ==
 
<syntaxhighlight lang="python">
 
<syntaxhighlight lang="python">
 
# load an antibody Fab from the PDB
 
# load an antibody Fab from the PDB
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<gallery heights="240px" widths="340px">
 
<gallery heights="240px" widths="340px">
Image:elbow_angle_1.png|Fab fragment 3ghe shown with draw=1.
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Image:elbow_angle_3ghe.png|Fab fragment 3ghe shown with draw=1.
 
Image:elbow_angle_2.png|5 PDB examples from Stanfield, et al., JMB 2006, shown in the same orientation as in Figure 1 of that paper.
 
Image:elbow_angle_2.png|5 PDB examples from Stanfield, et al., JMB 2006, shown in the same orientation as in Figure 1 of that paper.
 
</gallery>
 
</gallery>

Revision as of 18:37, 8 June 2012

Type Python Script
Download elbow_angle.py
Author(s) Jared Sampson
License GPLv3
This code has been put under version control in the project Pymol-script-repo

Introduction

This script allows you to calculate the elbow angle of an antibody Fab fragment object and optionally draw a graphical representation of the vectors used to calculate the elbow angle.

Examples

# load an antibody Fab from the PDB
fetch 3ghe, async=0

# get a nice orientation
orient

# calculate the elbow angle and draw the vectors
elbow_angle 3ghe, draw=1

The black "dumbbells" pass through the centers of mass of the combined variable and constant domains, respectively. The green and red dumbbell denotes the residues used to split the variable and constant domains, with a green ball for the light chain, and a red ball for the heavy chain.