Read libraries from system resource. Wattos started at: January 19, 2007 10:19:24 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/pdb1s34.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 10980 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 932 Found number of new bond candidates: 787 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 23(C ) 1 1 1 2.970 159.632 5 N2 1(G ) 1 O2 23(C ) 1 1 1 2.950 153.025 5 N1 2(G ) 1 N3 22(C ) 1 1 1 2.888 171.119 5 N2 2(G ) 1 O2 22(C ) 1 1 1 3.001 161.850 5 N1 3(G ) 1 N3 21(C ) 1 1 1 2.956 157.763 5 N2 3(G ) 1 O2 21(C ) 1 1 1 2.939 166.636 5 N1 4(G ) 1 O2 20(U ) 1 1 1 2.950 162.873 5 N6 5(A ) 1 O4 19(U ) 1 1 1 2.979 163.871 5 N1 6(G ) 1 N3 18(C ) 1 1 1 3.009 168.646 5 N2 6(G ) 1 O2 18(C ) 1 1 1 3.016 158.881 5 N1 8(G ) 1 N3 17(C ) 1 1 1 2.898 150.220 5 N2 8(G ) 1 O2 17(C ) 1 1 1 2.874 142.120 5 N1 9(G ) 1 O2 16(U ) 1 1 1 2.924 159.734 5 N3 10(U ) 1 N1 15(A ) 1 1 1 2.964 148.020 5 N6 15(A ) 1 O4 10(U ) 1 1 1 2.937 174.380 5 N3 16(U ) 1 O6 9(G ) 1 1 1 2.961 174.895 5 N4 17(C ) 1 O6 8(G ) 1 1 1 2.958 147.938 5 N4 18(C ) 1 O6 6(G ) 1 1 1 2.931 175.219 5 N3 19(U ) 1 N1 5(A ) 1 1 1 2.906 162.064 5 N3 20(U ) 1 O6 4(G ) 1 1 1 2.999 170.588 5 N4 21(C ) 1 O6 3(G ) 1 1 1 2.924 156.437 5 N4 22(C ) 1 O6 2(G ) 1 1 1 2.977 156.496 5 N4 23(C ) 1 O6 1(G ) 1 1 1 2.943 161.424 5 N4 23(C ) 1 N4 22(C ) 1 1 1 2.788 93.741 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, 1s34_wc.csv] Trying to match bases to eachother for number of bases: 23 Considering number of hydrogen bonds: 24 Results contains number of sets of co-planar bases: 7 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 23( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 22( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( G) Mol: 1 Model: 1 Entry: 1 Residue: 21( C) Mol: 1 Model: 1 Entry: 1 Residue: 5( A) Mol: 1 Model: 1 Entry: 1 Residue: 19( U) Mol: 1 Model: 1 Entry: 1 Residue: 6( G) Mol: 1 Model: 1 Entry: 1 Residue: 18( C) 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: 10( U) Mol: 1 Model: 1 Entry: 1 Residue: 15( A) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1s34_wc.csv Wattos started at: January 19, 2007 10:19:24 AM CST Wattos stopped at: January 19, 2007 10:19:29 AM CST Wattos took (#ms): 5015