Read libraries from system resource. Wattos started at: January 19, 2007 10:17:34 AM CST 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/pdb1m82.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 24707 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 976 Found number of new bond candidates: 857 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: 24 Found number of new hydrogen bonds: 24 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N1 1(G ) 1 N3 25(C ) 1 1 1 2.855 156.249 5 N2 1(G ) 1 O2 25(C ) 1 1 1 2.811 161.260 5 N1 2(G ) 1 N3 24(C ) 1 1 1 2.785 150.323 5 N2 2(G ) 1 O2 24(C ) 1 1 1 2.742 146.909 5 N6 3(A ) 1 O4 23(U ) 1 1 1 2.731 129.409 5 N6 4(A ) 1 O4 22(U ) 1 1 1 3.016 154.504 5 N1 5(G ) 1 O2 21(U ) 1 1 1 2.708 136.855 5 N4 6(C ) 1 O6 20(G ) 1 1 1 2.829 164.392 5 N1 8(G ) 1 N3 17(C ) 1 1 1 2.864 169.948 5 N2 8(G ) 1 O2 17(C ) 1 1 1 2.814 164.738 5 N1 9(G ) 1 N3 16(C ) 1 1 1 2.869 147.866 5 N2 9(G ) 1 O2 16(C ) 1 1 1 2.825 150.091 5 N4 10(C ) 1 O6 15(G ) 1 1 1 2.640 126.567 5 N1 15(G ) 1 N3 10(C ) 1 1 1 2.777 151.852 5 N2 15(G ) 1 O2 10(C ) 1 1 1 2.823 158.265 5 N4 16(C ) 1 O6 9(G ) 1 1 1 2.808 124.828 5 N4 17(C ) 1 O6 8(G ) 1 1 1 2.796 154.700 5 N1 20(G ) 1 N3 6(C ) 1 1 1 2.859 161.060 5 N2 20(G ) 1 O2 6(C ) 1 1 1 2.761 153.691 5 N3 21(U ) 1 O6 5(G ) 1 1 1 3.140 172.017 5 N3 22(U ) 1 N1 4(A ) 1 1 1 2.713 154.836 5 N3 23(U ) 1 N1 3(A ) 1 1 1 2.813 133.218 5 N4 24(C ) 1 O6 2(G ) 1 1 1 2.751 157.533 5 N4 25(C ) 1 O6 1(G ) 1 1 1 2.785 156.427 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, 1m82_wc.csv] Trying to match bases to eachother for number of bases: 25 Considering number of hydrogen bonds: 24 Results contains number of sets of co-planar bases: 8 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 25( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 24( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( A) Mol: 1 Model: 1 Entry: 1 Residue: 23( U) Mol: 1 Model: 1 Entry: 1 Residue: 4( A) Mol: 1 Model: 1 Entry: 1 Residue: 22( U) Mol: 1 Model: 1 Entry: 1 Residue: 6( C) Mol: 1 Model: 1 Entry: 1 Residue: 20( G) Mol: 1 Model: 1 Entry: 1 Residue: 8( G) Mol: 1 Model: 1 Entry: 1 Residue: 17( C) Mol: 1 Model: 1 Entry: 1 Residue: 9( G) Mol: 1 Model: 1 Entry: 1 Residue: 16( C) Mol: 1 Model: 1 Entry: 1 Residue: 10( C) Mol: 1 Model: 1 Entry: 1 Residue: 15( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1m82_wc.csv Wattos started at: January 19, 2007 10:17:34 AM CST Wattos stopped at: January 19, 2007 10:17:42 AM CST Wattos took (#ms): 7171