Read libraries from system resource. Wattos started at: January 19, 2007 10:20:03 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/pdb1xhp.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 10230 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1226 Found number of new bond candidates: 1102 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: 38 Found number of new hydrogen bonds: 38 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 32(C ) 1 1 1 2.979 175.491 5 N2 1(G ) 1 O2 32(C ) 1 1 1 2.913 170.593 5 N6 2(A ) 1 O4 31(U ) 1 1 1 2.992 172.583 5 N1 3(G ) 1 O2 30(U ) 1 1 1 2.940 169.766 5 N4 4(C ) 1 O6 29(G ) 1 1 1 2.907 168.775 5 N6 5(A ) 1 N3 28(C ) 1 1 1 2.899 145.640 5 N6 5(A ) 1 N4 28(C ) 1 1 1 2.802 140.718 5 N1 6(G ) 1 N3 27(C ) 1 1 1 2.915 168.880 5 N2 6(G ) 1 O2 27(C ) 1 1 1 2.944 168.103 5 N3 7(U ) 1 N1 26(A ) 1 1 1 2.878 171.404 5 N3 8(U ) 1 N1 25(A ) 1 1 1 2.970 176.179 5 N4 9(C ) 1 O6 24(G ) 1 1 1 2.838 145.204 5 N4 10(C ) 1 N6 22(A ) 1 1 1 2.992 142.967 5 N4 11(C ) 1 O6 21(G ) 1 1 1 2.912 168.800 5 N4 12(C ) 1 O6 20(G ) 1 1 1 2.922 175.355 5 N3 13(U ) 1 N1 19(A ) 1 1 1 2.956 157.488 5 N2 14(G ) 1 N7 18(A ) 1 1 1 2.975 151.915 5 N6 18(A ) 1 N3 14(G ) 1 1 1 2.750 134.036 5 N6 19(A ) 1 O4 13(U ) 1 1 1 2.947 161.583 5 N1 20(G ) 1 N3 12(C ) 1 1 1 2.975 175.903 5 N2 20(G ) 1 O2 12(C ) 1 1 1 2.905 168.142 5 N1 21(G ) 1 N3 11(C ) 1 1 1 2.973 172.536 5 N2 21(G ) 1 O2 11(C ) 1 1 1 2.910 175.806 5 N6 22(A ) 1 N3 10(C ) 1 1 1 2.897 159.576 5 N6 22(A ) 1 N4 10(C ) 1 1 1 2.992 132.433 5 N1 24(G ) 1 O2 9(C ) 1 1 1 3.055 144.462 5 N1 24(G ) 1 N3 9(C ) 1 1 1 2.884 148.753 5 N2 24(G ) 1 O2 9(C ) 1 1 1 2.867 155.994 5 N6 25(A ) 1 O4 8(U ) 1 1 1 2.965 161.647 5 N6 26(A ) 1 O4 7(U ) 1 1 1 3.018 175.651 5 N4 27(C ) 1 O6 6(G ) 1 1 1 2.905 158.054 5 N4 28(C ) 1 N6 5(A ) 1 1 1 2.802 145.634 5 N4 28(C ) 1 N4 27(C ) 1 1 1 2.678 92.643 5 N1 29(G ) 1 N3 4(C ) 1 1 1 2.970 170.122 5 N2 29(G ) 1 O2 4(C ) 1 1 1 2.909 174.357 5 N3 30(U ) 1 O6 3(G ) 1 1 1 2.963 164.414 5 N3 31(U ) 1 N1 2(A ) 1 1 1 2.899 170.976 5 N4 32(C ) 1 O6 1(G ) 1 1 1 2.912 170.660 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, 1xhp_wc.csv] Trying to match bases to eachother for number of bases: 32 Considering number of hydrogen bonds: 38 Results contains number of sets of co-planar bases: 10 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 32( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( A) Mol: 1 Model: 1 Entry: 1 Residue: 31( U) Mol: 1 Model: 1 Entry: 1 Residue: 4( C) Mol: 1 Model: 1 Entry: 1 Residue: 29( G) Mol: 1 Model: 1 Entry: 1 Residue: 6( G) Mol: 1 Model: 1 Entry: 1 Residue: 27( C) Mol: 1 Model: 1 Entry: 1 Residue: 7( U) Mol: 1 Model: 1 Entry: 1 Residue: 26( A) Mol: 1 Model: 1 Entry: 1 Residue: 8( U) Mol: 1 Model: 1 Entry: 1 Residue: 25( A) Mol: 1 Model: 1 Entry: 1 Residue: 9( C) Mol: 1 Model: 1 Entry: 1 Residue: 24( G) Mol: 1 Model: 1 Entry: 1 Residue: 11( C) Mol: 1 Model: 1 Entry: 1 Residue: 21( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( C) Mol: 1 Model: 1 Entry: 1 Residue: 20( G) Mol: 1 Model: 1 Entry: 1 Residue: 13( U) Mol: 1 Model: 1 Entry: 1 Residue: 19( A) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1xhp_wc.csv Wattos started at: January 19, 2007 10:20:03 AM CST Wattos stopped at: January 19, 2007 10:20:09 AM CST Wattos took (#ms): 6026