Read libraries from system resource. Wattos started at: April 20, 2007 11:51:15 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/pdb1n8c.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 8019 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 883 Found number of new bond candidates: 787 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: 30 Found number of new hydrogen bonds: 30 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N4 1(C ) 1 O6 11(G ) 2 1 1 2.829 171.131 5 N1 2(G ) 1 N3 10(C ) 2 1 1 2.873 166.940 5 N2 2(G ) 1 O2 10(C ) 2 1 1 2.761 168.923 5 N1 3(G ) 1 N3 9(C ) 2 1 1 2.912 175.886 5 N2 3(G ) 1 O2 9(C ) 2 1 1 2.877 178.246 5 N3 4(T ) 1 N1 8(A ) 2 1 1 2.854 169.847 5 N4 5(C ) 1 O6 7(G ) 2 1 1 2.865 174.478 5 N6 6(A ) 1 O4 6(T ) 2 1 1 3.223 175.691 5 N4 7(C ) 1 O6 5(G ) 2 1 1 2.883 176.561 5 N1 8(G ) 1 N3 4(C ) 2 1 1 2.873 172.665 5 N2 8(G ) 1 O2 4(C ) 2 1 1 2.815 172.585 5 N6 9(A ) 1 O4 3(T ) 2 1 1 2.855 175.100 5 N1 10(G ) 1 N3 2(C ) 2 1 1 2.855 172.262 5 N2 10(G ) 1 O2 2(C ) 2 1 1 2.830 174.264 5 N1 11(G ) 1 N3 1(C ) 2 1 1 2.851 169.167 5 N2 11(G ) 1 O2 1(C ) 2 1 1 2.828 174.467 5 N4 1(C ) 2 O6 11(G ) 1 1 1 2.853 163.316 5 N4 2(C ) 2 O6 10(G ) 1 1 1 2.791 167.366 5 N3 3(T ) 2 N1 9(A ) 1 1 1 2.845 174.294 5 N4 4(C ) 2 O6 8(G ) 1 1 1 2.827 170.721 5 N1 5(G ) 2 N3 7(C ) 1 1 1 2.861 168.407 5 N2 5(G ) 2 O2 7(C ) 1 1 1 2.767 170.903 5 N3 6(T ) 2 N1 6(A ) 1 1 1 2.903 169.007 5 N1 7(G ) 2 N3 5(C ) 1 1 1 2.836 169.875 5 N2 7(G ) 2 O2 5(C ) 1 1 1 2.728 168.822 5 N6 8(A ) 2 O4 4(T ) 1 1 1 2.876 171.972 5 N4 9(C ) 2 O6 3(G ) 1 1 1 2.789 171.733 5 N4 10(C ) 2 O6 2(G ) 1 1 1 2.833 177.160 5 N1 11(G ) 2 N3 1(C ) 1 1 1 2.892 171.407 5 N2 11(G ) 2 O2 1(C ) 1 1 1 2.805 173.782 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, 1n8c_wc.csv] Trying to match bases to eachother for number of bases: 22 Considering number of hydrogen bonds: 30 Results contains number of sets of co-planar bases: 11 Results: Residue: 1( C) Mol: 1 Model: 1 Entry: 1 Residue: 11( G) Mol: 2 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 10( C) Mol: 2 Model: 1 Entry: 1 Residue: 3( G) Mol: 1 Model: 1 Entry: 1 Residue: 9( C) Mol: 2 Model: 1 Entry: 1 Residue: 4( T) Mol: 1 Model: 1 Entry: 1 Residue: 8( A) Mol: 2 Model: 1 Entry: 1 Residue: 5( C) Mol: 1 Model: 1 Entry: 1 Residue: 7( G) Mol: 2 Model: 1 Entry: 1 Residue: 6( A) Mol: 1 Model: 1 Entry: 1 Residue: 6( T) Mol: 2 Model: 1 Entry: 1 Residue: 7( C) Mol: 1 Model: 1 Entry: 1 Residue: 5( G) Mol: 2 Model: 1 Entry: 1 Residue: 8( G) Mol: 1 Model: 1 Entry: 1 Residue: 4( C) Mol: 2 Model: 1 Entry: 1 Residue: 9( A) Mol: 1 Model: 1 Entry: 1 Residue: 3( T) Mol: 2 Model: 1 Entry: 1 Residue: 10( G) Mol: 1 Model: 1 Entry: 1 Residue: 2( C) Mol: 2 Model: 1 Entry: 1 Residue: 11( G) Mol: 1 Model: 1 Entry: 1 Residue: 1( C) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1n8c_wc.csv Wattos started at: April 20, 2007 11:51:15 AM CDT Wattos stopped at: April 20, 2007 11:51:20 AM CDT Wattos took (#ms): 4371