Inherently you want to calculate:
1. the approximately two-fold relationship between VH and VL
2. the approximately two-fold relationship between CL and CH1
You can use many programs for that (e.g. LSQMAN) but ideally you want a
program that will report Direction Cosines for the rotation axis in this
superimposition. Particularly wacky CDR conformations could conceivably
confuse automatic alignment programs so you could delete those. You
should check the superimposed alignments for sanity (e.g. correspondence
of the disulfide bonds).
Then calculate the elbow angle for the Fab from the dot product of the
direction cosines of VL:VH and CL:CH1.
Phil Jeffrey
Princeton
tarique khan wrote:
Dear all,
I am trying to calculate elbow angle of my fab structure using a online
software developed by Robyn L. Stanfield /et. al/. but it is giving a
solution with the following errors.
WARNING: rotation matrix contains significant additional contributions
WARNING: and deviates significantly from a pseudo-twofold 0.721
WARNING: rotation matrix contains significant additional contributions
WARNING: and deviates significantly from a pseudo-twofold : 0.726
WARNING: there have been deviations from expected values -
please read the log above!)
No guarantee that the calulated elbow angle is meaningful
The Elbow angle is probably 174.5 deg.
*Kindly suggest some other way of accurately, calculating elbow angle.*
regards.
Tarique khan
