Read libraries from system resource. Wattos started at: April 20, 2007 11:46:59 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/pdb1f5g.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 16900 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 776 Found number of new bond candidates: 700 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: 21 Found number of new hydrogen bonds: 21 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 10(C ) 2 1 1 2.965 170.157 5 N2 1(G ) 1 O2 10(C ) 2 1 1 2.855 171.514 5 N4 2(C ) 1 O6 9(G ) 2 1 1 2.931 167.554 5 N1 4(G ) 1 O6 7(G ) 2 1 1 2.878 152.747 5 N1 5(G ) 1 N3 6(C ) 2 1 1 2.979 170.821 5 N2 5(G ) 1 O2 6(C ) 2 1 1 2.913 174.029 5 N4 6(C ) 1 O6 5(G ) 2 1 1 2.918 172.976 5 N3 8(U ) 1 N1 3(A ) 2 1 1 3.086 153.072 5 N1 9(G ) 1 N3 2(C ) 2 1 1 2.938 167.595 5 N2 9(G ) 1 O2 2(C ) 2 1 1 2.859 168.969 5 N4 10(C ) 1 O6 1(G ) 2 1 1 2.969 170.016 5 N1 1(G ) 2 N3 10(C ) 1 1 1 2.965 170.189 5 N4 2(C ) 2 O6 9(G ) 1 1 1 2.933 167.877 5 N1 4(G ) 2 O6 7(G ) 1 1 1 2.874 152.741 5 N1 5(G ) 2 N3 6(C ) 1 1 1 2.980 169.965 5 N2 5(G ) 2 O2 6(C ) 1 1 1 2.916 173.555 5 N4 6(C ) 2 O6 5(G ) 1 1 1 2.915 171.724 5 N3 8(U ) 2 N1 3(A ) 1 1 1 3.074 155.951 5 N1 9(G ) 2 N3 2(C ) 1 1 1 2.937 167.508 5 N2 9(G ) 2 O2 2(C ) 1 1 1 2.860 169.140 5 N4 10(C ) 2 O6 1(G ) 1 1 1 2.969 169.457 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, 1f5g_wc.csv] Trying to match bases to eachother for number of bases: 20 Considering number of hydrogen bonds: 21 Results contains number of sets of co-planar bases: 6 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 10( C) Mol: 2 Model: 1 Entry: 1 Residue: 2( C) Mol: 1 Model: 1 Entry: 1 Residue: 9( G) Mol: 2 Model: 1 Entry: 1 Residue: 5( G) Mol: 1 Model: 1 Entry: 1 Residue: 6( C) Mol: 2 Model: 1 Entry: 1 Residue: 6( C) Mol: 1 Model: 1 Entry: 1 Residue: 5( G) Mol: 2 Model: 1 Entry: 1 Residue: 9( G) Mol: 1 Model: 1 Entry: 1 Residue: 2( C) Mol: 2 Model: 1 Entry: 1 Residue: 10( C) Mol: 1 Model: 1 Entry: 1 Residue: 1( G) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1f5g_wc.csv Wattos started at: April 20, 2007 11:46:59 AM CDT Wattos stopped at: April 20, 2007 11:47:05 AM CDT Wattos took (#ms): 5937