Protein secondary structure assignment from atomic coordinates D. Frishman & P. Argos Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins. 1995 Dec;23(4):566-79. protein:2d structure stride stride perl "stride" 0 pdbfile PDB File perl ($pdbid) ? " $pdbid.pdb" : " $value" 10 You must enter either the PDB data or the PDB id perl ! ($pdbid || $pdbfile) pdbid or you can instead enter a PDB id. perl (($pdbid =~ tr/A-Z/a-z/) || $value)? "cat `pdbloc $pdbid` > $pdbid.pdb ; " : "" -10 control Control parameters read_chain Read only these chains (-r) perl ($value)? " -r$value" : "" 1 Example: AB => calculate secondary structure assignment for chains A and B only. process_chain Process only these chains (-c) perl ($value)? " -c$value" : "" 1 Process only chains Id1, Id2 ...etc. Secondary structure assignment will be produced only for these chains, but other chains that are present will be taken into account while calculating residue accessible surface and detecting inter-chain hydrogen bonds and, possibly, interchain beta-sheets. By default all protein chains read are processed. Examples: Process only = ABC and Read only = C => calculate secondary structure assignment for chain C in the presence of chains A and B. output Output parameters molscript Generate a Molscript file (-m) perl ($value)? " -m$pdbfile.mol" : "" 0 1 ss_only Report secondary structure summary Only (-o) perl ($value)? " -o":"" 0 1 hydrogen Report Hydrogen bonds (-h) perl ($value)? " -h" : "" 0 1 fasta Generate SeQuence file in FASTA format (-q) perl ($value)? " -q" : "" 0 1 molscript_file perl $molscript *.mol outfile *.out stride_outfile perl 1