Read libraries from system resource. Wattos started at: April 20, 2007 11:48:48 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/pdb1k2k.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 378 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 466 Found number of new bond candidates: 406 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: 16 Found number of new hydrogen bonds: 16 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 6(G ) 2 1 1 2.850 168.374 5 N1 2(G ) 1 N3 5(C ) 2 1 1 2.828 169.397 5 N2 2(G ) 1 O2 5(C ) 2 1 1 2.837 169.259 5 N3 3(T ) 1 N1 4(A ) 2 1 1 2.826 169.304 5 N6 4(A ) 1 O4 3(T ) 2 1 1 2.859 169.307 5 N4 5(C ) 1 O6 2(G ) 2 1 1 2.857 168.673 5 N1 6(G ) 1 N3 1(C ) 2 1 1 2.848 167.988 5 N2 6(G ) 1 O2 1(C ) 2 1 1 2.823 168.901 5 N4 1(C ) 2 O6 6(G ) 1 1 1 2.851 168.392 5 N1 2(G ) 2 N3 5(C ) 1 1 1 2.828 169.392 5 N2 2(G ) 2 O2 5(C ) 1 1 1 2.837 169.257 5 N3 3(T ) 2 N1 4(A ) 1 1 1 2.826 169.266 5 N6 4(A ) 2 O4 3(T ) 1 1 1 2.860 169.220 5 N4 5(C ) 2 O6 2(G ) 1 1 1 2.857 168.714 5 N1 6(G ) 2 N3 1(C ) 1 1 1 2.849 167.966 5 N2 6(G ) 2 O2 1(C ) 1 1 1 2.823 168.825 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, 1k2k_wc.csv] Trying to match bases to eachother for number of bases: 12 Considering number of hydrogen bonds: 16 Results contains number of sets of co-planar bases: 6 Results: Residue: 1( C) Mol: 1 Model: 1 Entry: 1 Residue: 6( G) Mol: 2 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 5( C) Mol: 2 Model: 1 Entry: 1 Residue: 3( T) Mol: 1 Model: 1 Entry: 1 Residue: 4( A) Mol: 2 Model: 1 Entry: 1 Residue: 4( A) Mol: 1 Model: 1 Entry: 1 Residue: 3( T) Mol: 2 Model: 1 Entry: 1 Residue: 5( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 2 Model: 1 Entry: 1 Residue: 6( G) Mol: 1 Model: 1 Entry: 1 Residue: 1( C) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1k2k_wc.csv Wattos started at: April 20, 2007 11:48:48 AM CDT Wattos stopped at: April 20, 2007 11:48:50 AM CDT Wattos took (#ms): 1955