Read libraries from system resource. Wattos started at: January 19, 2007 10:20:46 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/pdb1z30.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 8625 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 695 Found number of new bond candidates: 619 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 N1 1(G ) 1 N3 18(C ) 1 1 1 2.946 172.949 5 N2 1(G ) 1 O2 18(C ) 1 1 1 2.858 172.846 5 N1 2(G ) 1 O2 17(U ) 1 1 1 2.813 162.369 5 N4 3(C ) 1 O6 16(G ) 1 1 1 2.948 170.879 5 N1 4(G ) 1 N3 15(C ) 1 1 1 2.931 168.682 5 N2 4(G ) 1 O2 15(C ) 1 1 1 2.882 176.711 5 N3 5(U ) 1 N1 14(A ) 1 1 1 2.981 170.215 5 N3 6(U ) 1 N1 13(A ) 1 1 1 3.012 170.576 5 N4 7(C ) 1 O6 12(G ) 1 1 1 2.954 164.697 5 N1 12(G ) 1 N3 7(C ) 1 1 1 2.949 165.121 5 N2 12(G ) 1 O2 7(C ) 1 1 1 2.864 168.660 5 N6 13(A ) 1 O4 6(U ) 1 1 1 2.933 165.965 5 N6 14(A ) 1 O4 5(U ) 1 1 1 2.926 170.559 5 N4 15(C ) 1 O6 4(G ) 1 1 1 2.950 174.799 5 N1 16(G ) 1 N3 3(C ) 1 1 1 2.941 172.638 5 N2 16(G ) 1 O2 3(C ) 1 1 1 2.857 169.148 5 N3 17(U ) 1 O6 2(G ) 1 1 1 3.074 179.741 5 N4 18(C ) 1 O6 1(G ) 1 1 1 2.898 161.420 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, 1z30_wc.csv] Trying to match bases to eachother for number of bases: 18 Considering number of hydrogen bonds: 18 Results contains number of sets of co-planar bases: 6 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 18( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( C) Mol: 1 Model: 1 Entry: 1 Residue: 16( G) Mol: 1 Model: 1 Entry: 1 Residue: 4( G) Mol: 1 Model: 1 Entry: 1 Residue: 15( C) Mol: 1 Model: 1 Entry: 1 Residue: 5( U) Mol: 1 Model: 1 Entry: 1 Residue: 14( A) Mol: 1 Model: 1 Entry: 1 Residue: 6( U) Mol: 1 Model: 1 Entry: 1 Residue: 13( A) Mol: 1 Model: 1 Entry: 1 Residue: 7( C) Mol: 1 Model: 1 Entry: 1 Residue: 12( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1z30_wc.csv Wattos started at: January 19, 2007 10:20:46 AM CST Wattos stopped at: January 19, 2007 10:20:49 AM CST Wattos took (#ms): 3720