Elbow angle - Revision history

Bell: 1 revision

2014-09-16T03:26:32Z

1 revision

2014-08-13T18:47:55Z

Syntax: added rationale for default limit residues

2014-03-28T02:00:38Z

25 revisions

2013-11-06T17:41:55Z

Basic usage: added link to COM

2012-10-05T21:01:23Z

Syntax

2012-06-15T19:14:34Z

Included Example: added user link

2012-06-15T19:13:55Z

changed release license to BSD

2012-06-15T19:13:11Z

Included Example: converted to infobox again (read that the old template had been deprecated)

2012-06-15T19:05:57Z

Included Example: restored original infobox from PymolScriptRepoDownload template

2012-06-15T19:00:32Z

Included Example: moved infobox down to be in same place as included pml script source

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 The first argument should be a PyMOL object.  You can calculate the elbow angles of multiple Fabs from the same object (one at a time) by specifying the chains manually for each Fab.
-The light and heavy arguments are for PDB chain IDs, and limit_l and limit_h are the last residue of the light and heavy chain variable domains, respectively.  (These last two values can be estimated by visual inspection of the PDB file.)  Setting draw=1 will draw the "dumbbells" seen in the images below.
+The `light` and `heavy` arguments are for PDB chain IDs, and `limit_l` and `limit_h` are the last residue of the light and heavy chain variable domains, respectively.  (For Kabat-numbered structures, these limits will be 107 and 113, respectively.  For structures with different numbering schemes, the limits can be estimated by visual inspection of the PDB file.)  Setting `draw=1` will draw the "dumbbells" seen in the images below.
 == Examples ==

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 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>
-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.
+The black "dumbbells" pass through the centers of mass of the variable and constant domains of each Fab (as determined using [[com|com.py]]). 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.
 ===Included Example===

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 </syntaxhighlight>
-The first argument should be a PyMOL object.  You can calculate the elbow angles of multiple Fabs from the same object by specifying the chains manually for each Fab.
+The first argument should be a PyMOL object.  You can calculate the elbow angles of multiple Fabs from the same object (one at a time) by specifying the chains manually for each Fab.
 == Examples ==

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 |type      = pml
 |filename  = examples/elbow_angle.pml
-|author    = Jared Sampson
+|author    = [[User:jaredsampson|Jared Sampson]]
 |license   = BSD
 }}

@@ Line 3: / Line 3: @@
 |filename  = elbow_angle.py
 |author    = [[User:jaredsampson|Jared Sampson]]
-|license   = GPLv3
+|license   = BSD
 }}

← Older revision	Revision as of 03:26, 16 September 2014
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← Older revision	Revision as of 02:00, 28 March 2014
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 This will run the following .pml file:
-{{Template:PymolScriptRepoDownload|examples/elbow_angle.pml}}
+{{Infobox script-repo
 <include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/elbow_angle.pml" highlight="python" />