1application: psiphi [ 2 documentation: "Calculates phi and psi torsion angles from 3 protein coordinates" 4 groups: "protein:3D structure" 5 relations: "EDAM_topic:2814 Protein structure analysis" 6 relations: "EDAM_operation:0249 Torsion angle calculation" 7] 8 9section: input [ 10 information: "Input section" 11 type: "page" 12] 13 14 infile: infile [ 15 parameter: "Y" 16 information: "Clean protein structure coordinates file" 17 knowntype: "protein clean coordinates" 18 relations: "EDAM_data:1460 Protein structure" 19 ] 20 21endsection: input 22 23section: required [ 24 information: "Required section" 25 type: "page" 26] 27 28 integer: chainnumber [ 29 standard: "Y" 30 information: "Number of the chain for which torsion angles 31 should be calculated" 32 default: "1" 33 minimum: "1" 34 relations: "EDAM_identifier:1008 Polypeptide chain ID" 35 ] 36 37 integer: startresiduenumber [ 38 standard: "Y" 39 information: "First residue in chain for which torsion 40 angles should be calculated" 41 default: "1" 42 minimum: "1" 43 relations: "EDAM_data:1016 Sequence position" 44 ] 45 46 integer: finishresiduenumber [ 47 standard: "Y" 48 information: "Last residue in chain for which torsion 49 angles should be calculated (1 = last residue)" 50 default: "1" 51 relations: "EDAM_data:1016 Sequence position" 52 ] 53 54endsection: required 55 56section: advanced [ 57 information: "Advanced section" 58 type: "page" 59] 60 61endsection: advanced 62 63section: output [ 64 information: "Output section" 65 type: "page" 66] 67 68 report: outfile [ 69 parameter: "Y" 70 rformat: "table" 71 multiple: "N" 72 precision: "1" 73 taglist: "float:phi float:psi" 74 relations: "EDAM_data:1544 Ramachandran plot" 75 ] 76 77endsection: output 78