AVESTRUC

For various reasons, it is often useful to derive `average` structures (i.e. for homology modelling, molecular replacement search objects, etc.). STAMP output provides an obvious starting point for obtaining an average structure. AVESTRUC reads in a STAMP alignment file, and generates another PDB file containing averaged coordinates (either as C alpha or as a polyalanine structure).

The format is:

    avestruc -f <STAMP alignment file> 
    [ -polyA -c <STAMP char> -t <threshold> -w <window> -aligned ]

`-f' specifies the file to be considered. Note that this MUST BE a STAMP alignment file, containing both transformations and a sequence alignment. It will not work on transformation files lacking sequence alignment data or STAMP data.

`-polyA' generate polyalanine model, the default is a C alpha model

`-c $<$STAMP char$>$' `-t $<$threshold$>$' `-w $<$window$>$'
these three parameters tell the program how to define structurally equivalent residues. `STAMP char' is the label of the STAMP field specified by the `#' character in the alignment file. `threshold' is the minimum (or maximum in the case of RMS deviation) value of the specified STAMP parameter tolerated, and `window' tells the minimum number of residues over which this must be true for structural equivalence. This is less complicated than it sounds.

The default is as described in [1]:
STAMP char = `G' (i.e. $P_{ij}{\prime}$)
threshold = 6.0
window = 3
(i.e. stretches of three or more residues having $P_{ij}{\prime} > 6.0$ are considered equivalent)

`-aligned' this flag will generate an averaged position for all positions structures are present at a position (i.e. positions not containing any gaps are deamed equivalent). The temperature factor will then distinguish between genuine structural equivalences and fortitously aligned residues.

`-ident' `-cons' these flags will name residues either as a single amino acid type (ident) or a conserved type (cons) according to the sequence alignment. See the appropriate sections in the preceding chapter for a further explanation.