Read libraries from system resource. Wattos started at: January 19, 2007 10:18:18 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/pdb1nc0.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 13896 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 956 Found number of new bond candidates: 832 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: 11 Found number of new hydrogen bonds: 11 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 24(C ) 1 1 1 3.009 163.467 5 N1 2(G ) 1 N3 23(C ) 1 1 1 2.793 160.769 5 N3 3(U ) 1 N1 22(A ) 1 1 1 2.878 156.970 5 N3 4(U ) 1 N1 21(A ) 1 1 1 3.015 177.064 5 N2 10(G ) 1 N7 14(A ) 1 1 1 3.202 159.952 5 N6 14(A ) 1 N3 10(G ) 1 1 1 2.607 125.033 5 N1 16(G ) 1 N3 8(C ) 1 1 1 2.957 163.157 5 N1 17(G ) 1 N3 7(C ) 1 1 1 3.021 164.048 5 N1 17(G ) 1 N4 7(C ) 1 1 1 3.247 134.810 5 N1 19(G ) 1 N3 6(C ) 1 1 1 2.844 163.097 5 N1 20(G ) 1 N3 5(C ) 1 1 1 2.918 158.922 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, 1nc0_wc.csv] Trying to match bases to eachother for number of bases: 24 Considering number of hydrogen bonds: 11 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: 1nc0_wc.csv Wattos started at: January 19, 2007 10:18:18 AM CST Wattos stopped at: January 19, 2007 10:18:21 AM CST Wattos took (#ms): 2414