Elbow angle

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

• Elbow angle 1.png

  Fab fragment 3ghe shown with draw=1.

• 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.

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.

Example 1

Download: examples/elbow_angle.pml

This code has been put under version control in the project Pymol-script-repo

reinitialize
import elbow_angle

bg_color white

# example structures from Stanfield, et al. JMB 2006
# doi:10.1016/j.jmb.2006.01.023
fetch 1bbd, async=0
fetch 7fab, async=0
fetch 1dba, async=0
fetch 1plg, async=0
fetch 1nl0, async=0

dss
as cartoon
set cartoon_transparency, 0.7

remove all and not chain L+H
util.mass_align("1bbd and ((chain L and resi 1-114) or (chain H and resi 1-118))")

# adopt a similar view to Figure 1 in Stanfield, et al.
set_view (\
    -0.953261435,   -0.226005003,    0.200535893,\
    -0.230026290,    0.112494141,   -0.966659248,\
     0.195909262,   -0.967606425,   -0.159222543,\
     0.000000000,    0.000000000, -230.122619629,\
    62.279075623,   48.879341125,  138.177505493,\
   181.430419922,  278.814819336,  -20.000000000 )

# 1bbd
# Stanfield:      127 deg
# elbow_angle.py: 125 deg
elbow_angle 1bbd, limit_l=114, limit_h=118, draw=1

# 7fab
# Stanfield:      132 deg
# elbow_angle.py: 126 deg
elbow_angle 7fab, limit_l=104, limit_h=117, draw=1

# 1dba
# Stanfield:      183 deg
# elbow_angle.py: 176 deg
elbow_angle 1dba, draw=1

# 1plg
# Stanfield:      190 deg
# elbow_angle.py: 189 deg
elbow_angle 1plg, limit_l=112, limit_h=117, draw=1

# 1nl0
# Stanfield:      220 deg
# elbow_angle.py: 221 deg
elbow_angle 1nl0, draw=1