Read libraries from system resource. Wattos started at: April 20, 2007 11:45:47 AM CDT Program arguments [1] :[-at] SubMenus:----------------------------------------------------- File Edit View Options Prop - Attr Calc Help - Commands:----------------------------------------------------- - Read libraries from system resource. SubMenus:----------------------------------------------------- File Edit View Options Prop - Attr Calc Help - Commands:----------------------------------------------------- - SubMenus:----------------------------------------------------- File Edit View Options Prop - Attr Calc Help - Commands:----------------------------------------------------- - Enter property name: Enter property value (watch value type) for interactiveSession: Enter property name: Enter property value (watch value type) for verbosity: Enter property name: Enter property value (watch value type) for writeSessionOnExit: Enter property name: Enter property value (watch value type) for stopOnError: Enter url to (gzipped) PDB formatted coordinate file: Doing ReadEntryPDB with arguments: [file:/dumpzone/pdb/nozip/data/structures/all/pdb/pdb1b4y.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 11388 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1162 Found number of new bond candidates: 1015 Hydrogen bond distance between proton and acceptor cutoff (2.7 Angstroms suggested) Hydrogen bond distance between donor and acceptor cutoff (3.35 Angstroms suggested) Hydrogen bond angle (D-H-A) cutoff (90 degrees suggested) Doing CalcHydrogenBond with arguments: [2.7, 3.35, 90.0] Found number of new hydrogen bond candidates: 34 Found number of new hydrogen bonds: 34 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N3 1(T ) 1 N7 21(A ) 1 1 1 2.488 146.810 5 N3 2(C ) 1 N7 22(G ) 1 1 1 2.963 144.148 5 N4 2(C ) 1 O6 22(G ) 1 1 1 2.868 159.237 5 N3 3(T ) 1 N7 23(A ) 1 1 1 2.777 153.034 5 N3 4(T ) 1 N7 24(A ) 1 1 1 2.906 147.842 5 N3 5(C ) 1 N7 25(G ) 1 1 1 2.741 123.824 5 N4 5(C ) 1 O6 25(G ) 1 1 1 2.774 145.785 5 N3 6(C ) 1 N7 26(G ) 1 1 1 2.656 125.635 5 N4 6(C ) 1 N7 26(G ) 1 1 1 2.774 123.461 5 N4 6(C ) 1 O6 26(G ) 1 1 1 2.289 105.337 5 N4 11(C ) 1 O6 26(G ) 1 1 1 3.023 169.234 5 N4 12(C ) 1 O6 25(G ) 1 1 1 3.005 141.381 5 N4 12(C ) 1 N1 25(G ) 1 1 1 3.157 121.945 5 N3 13(T ) 1 N1 24(A ) 1 1 1 3.037 167.184 5 N3 14(T ) 1 N1 23(A ) 1 1 1 2.727 148.332 5 N4 15(C ) 1 O6 22(G ) 1 1 1 2.285 111.285 5 N4 15(C ) 1 N1 22(G ) 1 1 1 2.691 108.310 5 N3 16(T ) 1 N1 21(A ) 1 1 1 2.571 162.175 5 N3 17(C ) 1 N7 20(G ) 1 1 1 2.726 124.837 5 N4 17(C ) 1 O6 20(G ) 1 1 1 2.666 149.124 5 N6 21(A ) 1 O4 1(T ) 1 1 1 2.951 155.817 5 N6 21(A ) 1 O4 16(T ) 1 1 1 2.659 168.294 5 N1 22(G ) 1 N3 15(C ) 1 1 1 2.495 101.305 5 N1 22(G ) 1 N4 15(C ) 1 1 1 2.691 103.614 5 N2 22(G ) 1 N3 15(C ) 1 1 1 2.592 104.483 5 N6 23(A ) 1 O4 3(T ) 1 1 1 2.488 137.137 5 N6 23(A ) 1 O4 14(T ) 1 1 1 2.697 151.558 5 N6 24(A ) 1 O4 4(T ) 1 1 1 3.000 165.548 5 N6 24(A ) 1 O4 13(T ) 1 1 1 2.773 154.590 5 N1 25(G ) 1 N3 12(C ) 1 1 1 2.738 126.465 5 N1 25(G ) 1 N4 12(C ) 1 1 1 3.157 134.542 5 N2 25(G ) 1 N3 12(C ) 1 1 1 2.687 128.049 5 N1 26(G ) 1 N3 11(C ) 1 1 1 2.712 153.718 5 N2 26(G ) 1 O2 11(C ) 1 1 1 2.371 132.283 5 Angle cutoff (40.0 degrees suggested) Use only Watson Crick basepairing (false suggested) (y/n): Enter cvs file name (with path) for output of CalcCoPlanarBasesSet.: Doing CalcCoPlanarBasesSet with arguments: [45.0, true, 1b4y_wc.csv] Trying to match bases to eachother for number of bases: 30 Considering number of hydrogen bonds: 34 Results contains number of sets of co-planar bases: 6 Results: Residue: 11( C) Mol: 1 Model: 1 Entry: 1 Residue: 26( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( C) Mol: 1 Model: 1 Entry: 1 Residue: 25( G) Mol: 1 Model: 1 Entry: 1 Residue: 13( T) Mol: 1 Model: 1 Entry: 1 Residue: 24( A) Mol: 1 Model: 1 Entry: 1 Residue: 14( T) Mol: 1 Model: 1 Entry: 1 Residue: 23( A) Mol: 1 Model: 1 Entry: 1 Residue: 15( C) Mol: 1 Model: 1 Entry: 1 Residue: 22( G) Mol: 1 Model: 1 Entry: 1 Residue: 16( T) Mol: 1 Model: 1 Entry: 1 Residue: 21( A) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1b4y_wc.csv Wattos started at: April 20, 2007 11:45:47 AM CDT Wattos stopped at: April 20, 2007 11:45:52 AM CDT Wattos took (#ms): 4569