Read libraries from system resource. Wattos started at: January 19, 2007 10:21:18 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/pdb2dd2.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 17496 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 768 Found number of new bond candidates: 699 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: 19 Found number of new hydrogen bonds: 19 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 9(C ) 2 1 1 2.941 161.632 5 N2 1(G ) 1 O2 9(C ) 2 1 1 2.843 165.170 5 N1 2(G ) 1 N3 8(C ) 2 1 1 2.948 172.005 5 N2 2(G ) 1 O2 8(C ) 2 1 1 2.861 178.262 5 N2 4(G ) 1 N7 6(A ) 2 1 1 2.985 146.527 5 N1 7(G ) 1 N3 3(C ) 2 1 1 2.964 164.133 5 N2 7(G ) 1 O2 3(C ) 2 1 1 2.851 165.326 5 N1 8(G ) 1 N3 2(C ) 2 1 1 2.987 168.614 5 N2 8(G ) 1 O2 2(C ) 2 1 1 2.870 171.070 5 N4 9(C ) 1 O6 1(G ) 2 1 1 2.929 160.856 5 N1 1(G ) 2 N3 9(C ) 1 1 1 2.943 159.481 5 N2 1(G ) 2 O2 9(C ) 1 1 1 2.843 164.652 5 N4 2(C ) 2 O6 8(G ) 1 1 1 2.953 169.691 5 N4 3(C ) 2 O6 7(G ) 1 1 1 2.939 167.251 5 N2 4(G ) 2 N7 6(A ) 1 1 1 3.206 156.218 5 N6 6(A ) 2 O2* 4(G ) 1 1 1 2.981 164.347 5 N6 6(A ) 2 N3 4(G ) 1 1 1 3.049 149.846 5 N1 7(G ) 2 O2 3(U ) 1 1 1 2.808 164.283 5 N4 9(C ) 2 O6 1(G ) 1 1 1 2.913 164.839 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, 2dd2_wc.csv] Trying to match bases to eachother for number of bases: 19 Considering number of hydrogen bonds: 19 Results contains number of sets of co-planar bases: 5 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 9( C) Mol: 2 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 8( C) Mol: 2 Model: 1 Entry: 1 Residue: 7( G) Mol: 1 Model: 1 Entry: 1 Residue: 3( C) Mol: 2 Model: 1 Entry: 1 Residue: 8( G) Mol: 1 Model: 1 Entry: 1 Residue: 2( C) Mol: 2 Model: 1 Entry: 1 Residue: 9( C) Mol: 1 Model: 1 Entry: 1 Residue: 1( G) Mol: 2 Model: 1 Entry: 1 Writing results to file: 2dd2_wc.csv Wattos started at: January 19, 2007 10:21:18 AM CST Wattos stopped at: January 19, 2007 10:21:25 AM CST Wattos took (#ms): 7422