I am currently working on a project in which we aim to produce a thermo-labile receptor. in the course of my preliminary research I came across the B FITTER program which calculates the amino acid B-factor as an average of the B-factors of all of its atoms excluding hydrogen, then generates an output file with a ranked classification of all the residues according to the B-factor. (described here: Reetz MT, Carballeira JD. 2007. Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat Protoc 2:891–903.)
My problem is that some of the PDB files generate a proper output file, while others turn up a blank file (example: 3K90 produces a proper file, while 3KB0 doesn't). Could this be caused by a difference in the PDB file format? is there a way around this issue?
Many thanks in advance,
Dan.
Although I am not familiar with B FITTER, my guess would be the following:
3K90 contains only isotropic B-factors, while 3KB0 contain the more informative anisotropic B-factors. Isotropic B-factors are listed in the ATOM records of a PDB file, while anisotropic B-factors have their own ANISOU records. Look at the pdb files in a text editor to see the difference, and check whether other problematic files also use anisotropic B-factors. see https://www.phenix-online.org/documentation/dictionary.html for a definition/image of the difference between isotropic and anisotropic B-factors.
Annemarie Honegger
That was a very good guess! :)
I removed the ANISOU records from the file, and my problem was solved.
I learned a few new things following your answer, thank you for your help!
In case anyone comes across this thread in the future, I selectively removed the ANISOU records using a program called PDBest:
http://www.pdbest.dcc.ufmg.br/
The inclusion of some unrecognised elements in the latter PDB may lead to such problems.
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