Read libraries from system resource. Wattos started at: January 19, 2007 10:17:44 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/pdb1mfy.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 15840 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1233 Found number of new bond candidates: 1066 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: 18 Found number of new hydrogen bonds: 18 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N3 3(U ) 1 O6 29(G ) 1 1 1 3.043 144.326 5 N1 5(G ) 1 N3 28(C ) 1 1 1 3.067 161.714 5 N2 5(G ) 1 O2 28(C ) 1 1 1 3.158 168.745 5 N6 6(A ) 1 O4 27(U ) 1 1 1 2.834 162.464 5 N6 7(A ) 1 O4 26(U ) 1 1 1 2.933 177.580 5 N1 12(G ) 1 N3 21(C ) 1 1 1 3.077 164.072 5 N2 12(G ) 1 O2 21(C ) 1 1 1 3.222 150.596 5 N1 13(G ) 1 N3 20(C ) 1 1 1 3.086 169.180 5 N2 13(G ) 1 O2 20(C ) 1 1 1 3.248 155.349 5 N4 14(C ) 1 O6 19(G ) 1 1 1 2.851 154.341 5 N1 19(G ) 1 N3 14(C ) 1 1 1 3.065 158.481 5 N2 19(G ) 1 O2 14(C ) 1 1 1 3.161 167.202 5 N4 20(C ) 1 O6 13(G ) 1 1 1 2.909 178.277 5 N4 21(C ) 1 O6 12(G ) 1 1 1 2.909 176.496 5 N3 26(U ) 1 N1 7(A ) 1 1 1 3.089 163.588 5 N3 27(U ) 1 N1 6(A ) 1 1 1 2.801 153.766 5 N4 28(C ) 1 O6 5(G ) 1 1 1 2.886 161.662 5 N1 29(G ) 1 O2 3(U ) 1 1 1 3.193 166.441 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, 1mfy_wc.csv] Trying to match bases to eachother for number of bases: 31 Considering number of hydrogen bonds: 18 Results contains number of sets of co-planar bases: 6 Results: Residue: 5( G) Mol: 1 Model: 1 Entry: 1 Residue: 28( C) Mol: 1 Model: 1 Entry: 1 Residue: 6( A) Mol: 1 Model: 1 Entry: 1 Residue: 27( U) Mol: 1 Model: 1 Entry: 1 Residue: 7( A) Mol: 1 Model: 1 Entry: 1 Residue: 26( U) Mol: 1 Model: 1 Entry: 1 Residue: 12( G) Mol: 1 Model: 1 Entry: 1 Residue: 21( C) Mol: 1 Model: 1 Entry: 1 Residue: 13( G) Mol: 1 Model: 1 Entry: 1 Residue: 20( C) Mol: 1 Model: 1 Entry: 1 Residue: 14( C) Mol: 1 Model: 1 Entry: 1 Residue: 19( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1mfy_wc.csv Wattos started at: January 19, 2007 10:17:44 AM CST Wattos stopped at: January 19, 2007 10:17:50 AM CST Wattos took (#ms): 6054