[ccp4bb] problem in calculation of elbow angle.
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-twofold0.721 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
Re: [ccp4bb] problem in calculation of elbow angle.
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-twofold0.721 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
Re: [ccp4bb] problem in calculation of elbow angle.
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(b...@ruppweb.orgmailto:b...@ruppweb.org) Cheers, Robyn ro...@scripps.edu From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of tarique khan Sent: Wednesday, January 13, 2010 4:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] problem in calculation of elbow angle. 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-twofold0.721 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
