4.2 avestruc Russel, Barton avestruc avestruc seqlab avestruc perl "avestruc" 0 aligfile Alignment file produced by stamp (-f) perl " -f $value" 1 This must be a STAMP alignment file, containing both transformations and a sequence alignment. It will not work on transformation files lacking sequence alignment data or STAMP data. stamp_alig_file perl 1 average average.pdb polyA Generate polyalanine model (the default is a C alpha model) (-polyA) perl ($value)? " -polyA" : "" 2 stamp_char STAMP char (-c) perl ($value && $value ne $vdef)? " -c $value" : "" G 2 STAMP char is the label of the STAMP field specified by the `#' character in the alignment file. threshold Threshold (-t) perl (defined $value && $value != $vdef)? " -t $value" : "" 6.0 2 threshold is the minimum (or maximum in the case of RMS deviation) value of the specified STAMP parameter tolerated. window Window (-w) perl (defined $value && $value != $vdef)? " -w $value" : "" 3 2 Tells the minimum number of residues over which this must be true for structural equivalence. aligned Averaged position for all positions structures are present at a position (-aligned) perl ($value)? " -aligned" : "" 2 ident Name residues as a single amino acid type (-ident) perl ($value)? " -ident" : "" 2 cons Name residues as a conserved type (-cons) perl ($value)? " -cons" : "" 2