Read libraries from system resource. Wattos started at: April 20, 2007 11:52:09 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/pdb1np9.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 9944 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1131 Found number of new bond candidates: 972 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 4(G ) 1 O6 4(G ) 4 1 1 3.047 145.004 5 N2 4(G ) 1 N7 4(G ) 4 1 1 2.918 176.506 5 N1 5(G ) 1 O6 5(G ) 4 1 1 2.821 153.914 5 N2 5(G ) 1 N7 5(G ) 4 1 1 2.839 157.464 5 N1 6(G ) 1 O6 6(G ) 4 1 1 3.016 135.192 5 N2 6(G ) 1 N7 6(G ) 4 1 1 2.938 155.920 5 N1 4(G ) 2 O6 4(G ) 1 1 1 2.861 147.321 5 N2 4(G ) 2 N7 4(G ) 1 1 1 2.898 162.643 5 N1 5(G ) 2 O6 5(G ) 1 1 1 2.941 136.140 5 N2 5(G ) 2 N7 5(G ) 1 1 1 2.896 163.809 5 N1 6(G ) 2 O6 6(G ) 1 1 1 3.079 145.217 5 N2 6(G ) 2 N7 6(G ) 1 1 1 2.936 164.577 5 N6 3(A ) 3 N1 3(A ) 4 1 1 3.083 164.861 5 N1 4(G ) 3 O6 4(G ) 2 1 1 2.990 131.471 5 N2 4(G ) 3 N7 4(G ) 2 1 1 3.053 162.261 5 N1 5(G ) 3 O6 5(G ) 2 1 1 3.045 142.630 5 N2 5(G ) 3 N7 5(G ) 2 1 1 2.859 153.452 5 N1 6(G ) 3 O6 6(G ) 2 1 1 3.010 147.777 5 N2 6(G ) 3 N7 6(G ) 2 1 1 2.915 167.451 5 N1 4(G ) 4 O6 4(G ) 3 1 1 3.077 142.633 5 N2 4(G ) 4 N7 4(G ) 3 1 1 2.930 156.563 5 N1 5(G ) 4 O6 5(G ) 3 1 1 3.031 155.637 5 N2 5(G ) 4 N7 5(G ) 3 1 1 2.928 177.517 5 N1 6(G ) 4 O6 6(G ) 3 1 1 3.002 149.822 5 N2 6(G ) 4 N7 6(G ) 3 1 1 2.840 151.780 5 O3* 7(T ) 4 O4 7(T ) 3 1 1 2.673 171.844 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, 1np9_wc.csv] Trying to match bases to eachother for number of bases: 28 Considering number of hydrogen bonds: 26 WARNING: requested less than 1 new rows in getNewRowIdList: 0 Results contains number of sets of co-planar bases: 0 Results: Writing results to file: 1np9_wc.csv Wattos started at: April 20, 2007 11:52:09 AM CDT Wattos stopped at: April 20, 2007 11:52:11 AM CDT Wattos took (#ms): 2036