BAVERAGE (CCP4: Supported Program)
NAMEbaverage - averages B over main and side chain atoms
SYNOPSISbaverage XYZIN foo_in.pdb RMSTAB foo_out1.tab XYZOUT foo_out2.pdb
DESCRIPTIONA very simple minded program to read a PDB file, tabulate to RMSTAB the average B values residue by residue (main chain and side chain separately) and the RMS deviation of the B values from this mean. It also outputs a PDB file with outlying B factors reset to lie within the given range.
INPUT AND OUTPUT FILES
The available keywords are: TITLE, BLIMIT, BRANGE, END.
Title <title>Title to appear in output.
BLIMIT <bminmc> <bmaxmc> <bminsc> <bmaxsc>Reset B factors for XYZOUT to lie in given ranges.
BRANGE <brange>The output is also tarted up as a histogram showing the number of B values in ranges of width <brange> (default 5.0).
PROGRAM FUNCTIONI think this is a very useful way of monitoring possible errors in the structure. Although the absolute values are a function of the refinement protocol and the resolution of the data, spikes in the RMS values are often symptomatic of an error in the map interpretation. Usually such errors do not mean that the worker has fitted structure to empty regions; more often they have branched into density belonging to another residue or to well defined solvent. This can show up as large deviations in B values of adjacent atoms ; e.g. CB 22 CG 35 CD1 23 CD2 28 . where the CG is out of density, and the CDs actually occupy the space of a missing residue.
Unix example script found in $CEXAM/unix/runnable/
AUTHOREleanor Dodson: York 1991
SEE ALSOAlternative B factor analysis: