Read libraries from system resource. Wattos started at: January 19, 2007 10:17:06 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/pdb1kka.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 4384 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 706 Found number of new bond candidates: 591 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: 20 Found number of new hydrogen bonds: 20 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 17(C ) 1 1 1 3.197 160.754 5 N2 1(G ) 1 O2 17(C ) 1 1 1 3.119 150.422 5 N1 2(G ) 1 N3 16(C ) 1 1 1 3.201 169.802 5 N2 2(G ) 1 O2 16(C ) 1 1 1 3.150 154.689 5 N1 3(G ) 1 N3 15(C ) 1 1 1 3.217 165.465 5 N2 3(G ) 1 O2 15(C ) 1 1 1 3.158 166.034 5 N1 4(G ) 1 N3 14(C ) 1 1 1 3.143 150.633 5 N2 4(G ) 1 O2 14(C ) 1 1 1 3.114 145.918 5 N6 5(A ) 1 O4 13(U ) 1 1 1 3.066 162.002 5 N3 6(U ) 1 N1 12(A ) 1 1 1 3.095 151.057 5 N2 8(G ) 1 N6 9(A ) 1 1 1 3.076 122.972 5 N6 9(A ) 1 N2 8(G ) 1 1 1 3.076 127.562 5 N6 10(A ) 1 O2* 7(U ) 1 1 1 3.015 151.532 5 N6 10(A ) 1 O4* 8(G ) 1 1 1 2.822 116.650 5 N6 12(A ) 1 O4 6(U ) 1 1 1 3.217 174.221 5 N3 13(U ) 1 N1 5(A ) 1 1 1 2.977 129.767 5 N4 14(C ) 1 O6 4(G ) 1 1 1 3.041 143.676 5 N4 15(C ) 1 O6 3(G ) 1 1 1 3.165 168.526 5 N4 16(C ) 1 O6 2(G ) 1 1 1 3.216 176.380 5 N4 17(C ) 1 O6 1(G ) 1 1 1 3.205 166.608 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, 1kka_wc.csv] Trying to match bases to eachother for number of bases: 17 Considering number of hydrogen bonds: 20 Results contains number of sets of co-planar bases: 6 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 17( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 16( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( G) Mol: 1 Model: 1 Entry: 1 Residue: 15( C) Mol: 1 Model: 1 Entry: 1 Residue: 4( G) Mol: 1 Model: 1 Entry: 1 Residue: 14( C) Mol: 1 Model: 1 Entry: 1 Residue: 5( A) Mol: 1 Model: 1 Entry: 1 Residue: 13( U) Mol: 1 Model: 1 Entry: 1 Residue: 6( U) Mol: 1 Model: 1 Entry: 1 Residue: 12( A) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1kka_wc.csv Wattos started at: January 19, 2007 10:17:06 AM CST Wattos stopped at: January 19, 2007 10:17:09 AM CST Wattos took (#ms): 3141