Maximal Common 3D Substructure Searching M.Petitjean M.Petitjean, Interactive Maximal Common 3D Substructure Searching with the Combined SDM/RMS Algorithm. Comput.Chem.1998,22[6],pp.463-465. protein:3d structure CSR CSR perl "CSR < params" 0 param params endparams perl "\\n\\n" 10 params pdbfile File containing both molecules perl "$value\\n" 2 This file must contain BOTH molecules. See below the position parameters of each molecules. params pdbfile perl $file_format eq "PDB" file_format Input file format perl "$value\\n" PDB 1 HIN HIN: alchemy-type MDL MDL: Cambridge Crystallographic Model ML2 ML2: Mol2 SYBYL PDB PDB: Protein Data Bank or Nucleic Acid Data Bank BIO BIO: Biosym (MSI) params imol1 Position of the 1st molecule in the file (IMOL1) perl "$value" 1 4 params imol2 Position of the 2d molecule in the file (IMOL2) perl " $value" 2 5 params itermx How many iterations (ITERMX) perl " $value" 200 6 About 200 for a small molecule of less than 100 atoms, about 2000 for less than 1000 atoms, 20000 for more than 1000 atoms params cutoff Cutoff distance (CUT-OFF DIST) perl " $value\\n" 1.2 7 1.2 1.2: for a protein 2 2: for an inorganic molecule 5 5: for a C-alpha backbone. This parameter does not change the results, it just saves memory and space. params substructure perl "new_mol2.coord\\n" new_mol2.coord 3 params pdb_outfile new_mol2.coord pdbfile perl 1