BAVERAGE (CCP4: Supported Program)
- averages B over main and side chain atoms
A 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
- Input coordinates.
- Table of average B factors and rms deviations for
main chain (columns 2 and 3), side chain (columns 4 and 5) and
overall (columns 6 and 7). The residue number is given in column 1.
- Output coordinates with B values reset according to
The available keywords are: TITLE,
Title to appear in output.
BLIMIT <bminmc> <bmaxmc>
Reset B factors for XYZOUT to lie in given ranges.
The output is also tarted up as a histogram showing the number of B values
in ranges of width <brange> (default 5.0).
- minimum allowed value for the B value of a main chain atom (default 0.0).
- maximum allowed value for the B value of a main chain atom (default 100.0).
- minimum allowed value for the B value of a side chain atom (default 0.0).
- maximum allowed value for the B value of a side chain atom (default 100.0).
I 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/
Eleanor Dodson: York 1991
Alternative B factor analysis:
Graphical display of B factors: