The online COFACTOR provides TM-align results vs the complete PDB (not just the nr-PDB)
The standalone COFACTOR has the complete PDB functionality disabled, and only provides TM-align results vs nr-PDB
However, the standalone COFACTOR perl scripts have references to doing TM-align vs whole PDB (see COFACTORmod below).
I already have the necessary map library (NRPDB_PDBALL.map), and the complete PDB on my server (98544 .ent files).
In order to use TM-align vs complete PDB in standalone COFACTOR, do I need to reformat the original PDB (other than renaming .ent to .pdb)? In addition to the if (0) statement below, any other changes I should do to COFACTORmod to activate the use of PDBall?
Thanks in advance.
COFACTORmod code:
...
my $PDBlibrary ="$libdir/PDB/";
my $PDBall ="$libdir/PDBall";
...
#####Read NRPDB to PDBALL mapping
...
open(HOMOLOGS,"<$datdir/NRPDB_PDBALL.map");
...
print "Extend Search against NR-PDB to complete PDB...\n";
#########Extend Search against NR-PDB to complete PDB ##########################
...
if(0) #skip this part as PDBall is too big to be included in I-TASSER library
...
##### Run second round of TM-align search for re-ranking
printf "Extending TM-align search to complete PDB\n";
...