BAVERAGE (CCP4: Supported Program)

NAME

baverage - averages B over main and side chain atoms

SYNOPSIS

baverage XYZIN foo_in.pdb RMSTAB foo_out1.tab XYZOUT foo_out2.pdb
[Keyworded input]

DESCRIPTION

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

XYZIN: Input coordinates.
RMSTAB: 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.
XYZOUT: Output coordinates with B values reset according to keyword BLIMIT.

KEYWORDED INPUT

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.

<bminmc>: minimum allowed value for the B value of a main chain atom (default 0.0).
<bmaxmc>: maximum allowed value for the B value of a main chain atom (default 100.0).
<bminsc>: minimum allowed value for the B value of a side chain atom (default 0.0).
<bmaxsc>: maximum allowed value for the B value of a side chain atom (default 100.0).

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).

END

End input.

PROGRAM FUNCTION

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.

EXAMPLE

Unix example script found in $CEXAM/unix/runnable/

baverage.exam

AUTHOR

Eleanor Dodson: York 1991