Pdb2site reads a Protein Data Bank file and converts it to a site file suitable for input to dms. The -i argument specifies the input PDB_file. If no input file is given, pdb2site will read from standard input. The -o argument specifies the output site_file. If no output file is given, pdb2site will write to standard output.
Pdb2site is frequently used with pdbrun from within Chimera. *Note that when this is done, the PDB_file argument should not be supplied. The procedure is to display the atoms of interest and then type:
pdbrun pdb2site -o site_fileThis generates a file called site_file for input to dms with -i.