Read libraries from system resource. Wattos started at: January 19, 2007 10:18:56 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/pdb1pjy.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 14180 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 860 Found number of new bond candidates: 764 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: 26 Found number of new hydrogen bonds: 26 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 22(C ) 1 1 1 2.930 163.095 5 N2 1(G ) 1 O2 22(C ) 1 1 1 2.888 169.813 5 N1 2(G ) 1 N3 21(C ) 1 1 1 2.897 158.026 5 N2 2(G ) 1 O2 21(C ) 1 1 1 2.828 157.136 5 N4 3(C ) 1 O6 20(G ) 1 1 1 2.922 158.241 5 N4 4(C ) 1 O6 19(G ) 1 1 1 2.905 157.056 5 N3 5(U ) 1 N1 18(A ) 1 1 1 2.855 163.659 5 N3 6(U ) 1 N1 17(A ) 1 1 1 2.789 167.286 5 N4 7(C ) 1 O6 16(G ) 1 1 1 2.925 170.567 5 N4 8(C ) 1 O6 15(G ) 1 1 1 2.875 152.996 5 N4 9(C ) 1 O6 14(G ) 1 1 1 2.772 142.231 5 N6 13(A ) 1 N3 10(A ) 1 1 1 2.724 138.736 5 N1 14(G ) 1 N3 9(C ) 1 1 1 2.853 147.291 5 N2 14(G ) 1 O2 9(C ) 1 1 1 2.852 151.506 5 N1 15(G ) 1 N3 8(C ) 1 1 1 2.842 151.904 5 N2 15(G ) 1 O2 8(C ) 1 1 1 2.771 144.211 5 N1 16(G ) 1 N3 7(C ) 1 1 1 2.833 155.172 5 N2 16(G ) 1 O2 7(C ) 1 1 1 2.742 135.245 5 N6 17(A ) 1 O4 6(U ) 1 1 1 2.802 172.021 5 N6 18(A ) 1 O4 5(U ) 1 1 1 2.787 172.711 5 N1 19(G ) 1 N3 4(C ) 1 1 1 2.882 153.175 5 N2 19(G ) 1 O2 4(C ) 1 1 1 2.747 143.192 5 N1 20(G ) 1 N3 3(C ) 1 1 1 2.846 163.769 5 N2 20(G ) 1 O2 3(C ) 1 1 1 2.831 150.048 5 N4 21(C ) 1 O6 2(G ) 1 1 1 2.893 157.856 5 N4 22(C ) 1 O6 1(G ) 1 1 1 2.883 164.336 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, 1pjy_wc.csv] Trying to match bases to eachother for number of bases: 22 Considering number of hydrogen bonds: 26 Results contains number of sets of co-planar bases: 9 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 22( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 21( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( C) Mol: 1 Model: 1 Entry: 1 Residue: 20( G) Mol: 1 Model: 1 Entry: 1 Residue: 4( C) Mol: 1 Model: 1 Entry: 1 Residue: 19( G) Mol: 1 Model: 1 Entry: 1 Residue: 5( U) Mol: 1 Model: 1 Entry: 1 Residue: 18( A) Mol: 1 Model: 1 Entry: 1 Residue: 6( U) Mol: 1 Model: 1 Entry: 1 Residue: 17( A) Mol: 1 Model: 1 Entry: 1 Residue: 7( C) Mol: 1 Model: 1 Entry: 1 Residue: 16( G) Mol: 1 Model: 1 Entry: 1 Residue: 8( C) Mol: 1 Model: 1 Entry: 1 Residue: 15( G) Mol: 1 Model: 1 Entry: 1 Residue: 9( C) Mol: 1 Model: 1 Entry: 1 Residue: 14( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1pjy_wc.csv Wattos started at: January 19, 2007 10:18:56 AM CST Wattos stopped at: January 19, 2007 10:19:02 AM CST Wattos took (#ms): 5949