Difference between revisions of "Elbow angle"
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Jaredsampson (talk | contribs) (→Examples: updated gallery heights and widths) |
Jaredsampson (talk | contribs) (→Examples: Updated description of visualization, removed orient command from example.) |
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== Examples == | == Examples == | ||
<syntaxhighlight lang="python"> | <syntaxhighlight lang="python"> | ||
| + | |||
# load an antibody Fab from the PDB | # load an antibody Fab from the PDB | ||
fetch 3ghe, async=0 | fetch 3ghe, async=0 | ||
| − | |||
| − | |||
| − | |||
# calculate the elbow angle and draw the vectors | # calculate the elbow angle and draw the vectors | ||
elbow_angle 3ghe, draw=1 | elbow_angle 3ghe, draw=1 | ||
| + | |||
</syntaxhighlight> | </syntaxhighlight> | ||
| Line 25: | Line 24: | ||
Image:Stanfield.png|5 PDB examples from Stanfield, et al., JMB 2006, shown in the same orientations as in Figure 1 of that paper. | Image:Stanfield.png|5 PDB examples from Stanfield, et al., JMB 2006, shown in the same orientations as in Figure 1 of that paper. | ||
</gallery> | </gallery> | ||
| − | The black "dumbbells" pass through the centers of mass of the | + | The black "dumbbells" pass through the centers of mass of the variable and constant domains of each Fab. The green and red dumbbells denote 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. |
[[Category:Script_Library]] | [[Category:Script_Library]] | ||
[[Category:Structural_Biology_Scripts]] | [[Category:Structural_Biology_Scripts]] | ||
[[Category:Pymol-script-repo]] | [[Category:Pymol-script-repo]] | ||
Revision as of 14:54, 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
# calculate the elbow angle and draw the vectors
elbow_angle 3ghe, draw=1
Fab fragment 3ghe shown with draw=1.
5 PDB examples from Stanfield, et al., JMB 2006, shown in the same orientations as in Figure 1 of that paper.
The black "dumbbells" pass through the centers of mass of the variable and constant domains of each Fab. The green and red dumbbells denote 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.