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
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
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
A useful feature in AVESTRUC 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:
See Taylor (1986) for a description of amino acid properties.
Another new feature is that the tempeature factors now reflect whether postions are structural conserved, or simply fortitously 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 (e.g. with RasMol) the blue regions will correspond to those that are structural 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.