how to calculate elbow angle for Fabs

[schiweck at max.mpibp.uni-frankfurt.de]

In bionet xtallography msg # 2128 Jianping Ding writes :

-> Hi there,

-> Could anybody tell me if there are any programs that can
-> calculate the hinge (elbow) angle for Fab fragment?
-> Or other alternatives?

-> Thanks in advance!


-> Jianping Ding


Dear Jianping,

you can calculate the elbow angle of a Fab fragment as follows:

Superpose the VH domain on VL and CH on CL with LSQMAN (written by Gerard Kley-
wegt). After superpostion using the "show"-command, LSQMAN analyses the opera-
tors and calculates the direction cosines of the two pseudo-dyad axes. 
The angle between these two axes is then calculated using the general formula: 

cos THETA = cos ALPHA1 * cos ALPHA2 + cos BETA1 * cos BETA2 + cos GAMMA1 * cos
            GAMMA2  


If you also want to get the translational part of the superposition, for 
example the program CALC-AX (written by Joachim Meyer, University of Freiburg,
Germany,) does that job. Check the latest "O"-newsgroup contributions for his
program. 
  

Hope that helps


Wolfram Schiweck
Max-Planck-Institut fuer Biophysik
Heinrich-Hoffmann-Str. 7
60528 Frankfurt am Main
Germany
E-Mail: schiweck at max.mpibp.uni-frankfurt.de