Generating averaged coordinates

It may also be useful to have a set of averaged coordinates derived from a protein structural family. This makes it possible to see what portions of the structure are common to all members of the family (i.e. the common core). The program AVESTRUC takes the output from STAMP (i.e. an aligned family of protein structures), and generates a PDB file containing averaged coordinates for the common core as identified by STAMP. For example, to generate the averaged coordinates for the aspartic proteinase domains one needs to type:

avestruc -f ac_prot.8 -o ac_prot_ave.pdb

The file ac_prot_ave.pdb will contain a set of averaged ${\rm C}_{\alpha}$ atoms taken by averaging the coordinates for those positions within the file ac_prot.8 that are found to be structurally equivalent. To obtain a poly Alanine set of coordinates (i.e. including main chain and $C_{\beta}$ coordinates), type:

avestruc -f ac_prot.8 -o ac_prot_ave.pdb -polyA

Note that this will only work if all main chain atoms are found in the file (i.e. it won't work if the PDB files contain only ${\rm C}_{\alpha}$ atoms).

A useful feature in AVESTRUC that was added in STAMP version 4.1 is the use of the -ident and -cons options. The program now labels all residues in the averaged model as `UNK'. If positions are totally conserved across all structures in the averaged model, the `-ident' option will name residues accordingly. The -cons option will label residues additionally as conserved in character if all amino acids in the set have the following properties:

SMA	small
TIN	tiny
POL	polar
HYD	hydrophobic
POS	positive
NEG	negative
CHA	charged
ARO	aromatic
ALI	aliphatic
BRA	$C_{\beta}$ branched

See Taylor (1986) for a description of amino acid properties.

Another feature is that the temperature factors reflect whether postions are structurally conserved, or simply fortuitously aligned. If you add the option `-aligned' to the command line, all positions that are not matched to a gap will be considered in the generation of the averaged model. If you then colour your model according to temperature in a structure viewer, the blue regions will correspond to those that are structurally equivalent (as you have defined or by default) whereas the red regions will show those that are simply in the same position in the sequence alignment.