Dear Tarique,

 

   The elbow angle in a Fab is just the angle between two pseudo-twofold axes: one relating VL to VH and one relating CL to CH. You can find the pseudo-twofold axes using many different least-squares alignment programs, just pick your favorite. Then, just take the dot product of the two resulting axes/vectors for your elbow angle.  You can do this quite accurately with a pencil and paper and maybe a handheld calculator.

 

The error message you report indicates problems calculating the pseudo-two fold axes;  you probably either have (a) an unusual Fab where the axes relating light to heavy chains

deviate significantly from 180 degrees (b) a glitch or unusual feature in your  PDB file that has thrown off the calculation of the pseudo-two folds (thus making them appear to deviate from 180).  Bernhard might be able to enlighten you more as he wrote the code and error messages([log in to unmask])

 

Cheers,

Robyn

[log in to unmask]

 

 

 

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