Re: [ccp4bb] problem in calculation of elbow angle.

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: problem in calculation of elbow angle.
From: Bernhard Rupp br {- at -} RUPPWEB {- dot -} ORG
Date: 2010-01-13

Next message:
Subject: Reindexing P21.. the process?
From: Francis E Reyes Francis {- dot -} Reyes {- at -} COLORADO {- dot -} EDU
Date: 2010-01-13

Subject: Re: problem in calculation of elbow angle.
From: Robyn Stanfield robyn {- at -} SCRIPPS {- dot -} EDU
Date: 2010-01-13

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(br@ruppweb.org)

Cheers,

Robyn

robyn@scripps.edu

From: CCP4 bulletin board [mailto:CCP4BB@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-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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: problem in calculation of elbow angle.
From: Bernhard Rupp br {- at -} RUPPWEB {- dot -} ORG
Date: 2010-01-13

Next message:
Subject: Reindexing P21.. the process?
From: Francis E Reyes Francis {- dot -} Reyes {- at -} COLORADO {- dot -} EDU
Date: 2010-01-13