Read libraries from system resource. Wattos started at: April 20, 2007 11:48:01 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/pdb1jo7.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 31648 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1230 Found number of new bond candidates: 1065 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: 23 Found number of new hydrogen bonds: 23 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N6 1(A ) 1 O4 31(U ) 1 1 1 3.025 174.298 5 N1 2(G ) 1 N3 30(C ) 1 1 1 3.082 158.657 5 N2 2(G ) 1 O2 30(C ) 1 1 1 3.277 165.714 5 N6 4(A ) 1 O4 28(U ) 1 1 1 2.630 145.390 5 N6 6(A ) 1 O4 26(U ) 1 1 1 2.741 156.177 5 N6 7(A ) 1 O4 25(U ) 1 1 1 3.000 157.114 5 N4 9(C ) 1 O6 23(G ) 1 1 1 2.725 140.306 5 N1 12(G ) 1 N3 21(C ) 1 1 1 2.881 178.525 5 N2 12(G ) 1 O2 21(C ) 1 1 1 2.944 169.901 5 N1 13(G ) 1 N3 20(C ) 1 1 1 3.048 169.586 5 N2 13(G ) 1 O2 20(C ) 1 1 1 3.301 170.007 5 N4 14(C ) 1 O6 19(G ) 1 1 1 2.494 116.250 5 N1 19(G ) 1 N3 14(C ) 1 1 1 2.709 122.039 5 N2 19(G ) 1 O2 14(C ) 1 1 1 3.232 149.882 5 N4 20(C ) 1 O6 13(G ) 1 1 1 2.757 157.371 5 N4 21(C ) 1 O6 12(G ) 1 1 1 2.703 132.561 5 N1 23(G ) 1 N3 9(C ) 1 1 1 2.891 161.425 5 N2 23(G ) 1 O2 9(C ) 1 1 1 3.292 172.403 5 N3 25(U ) 1 N1 7(A ) 1 1 1 2.752 167.450 5 N3 26(U ) 1 N1 6(A ) 1 1 1 2.743 161.787 5 N3 28(U ) 1 N1 4(A ) 1 1 1 3.137 171.432 5 N4 30(C ) 1 O6 2(G ) 1 1 1 2.784 149.243 5 N3 31(U ) 1 N1 1(A ) 1 1 1 3.124 170.770 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, 1jo7_wc.csv] Trying to match bases to eachother for number of bases: 31 Considering number of hydrogen bonds: 23 Results contains number of sets of co-planar bases: 9 Results: Residue: 1( A) Mol: 1 Model: 1 Entry: 1 Residue: 31( U) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 30( C) Mol: 1 Model: 1 Entry: 1 Residue: 4( A) Mol: 1 Model: 1 Entry: 1 Residue: 28( U) Mol: 1 Model: 1 Entry: 1 Residue: 6( A) Mol: 1 Model: 1 Entry: 1 Residue: 26( U) Mol: 1 Model: 1 Entry: 1 Residue: 7( A) Mol: 1 Model: 1 Entry: 1 Residue: 25( U) Mol: 1 Model: 1 Entry: 1 Residue: 9( C) Mol: 1 Model: 1 Entry: 1 Residue: 23( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( G) Mol: 1 Model: 1 Entry: 1 Residue: 21( C) Mol: 1 Model: 1 Entry: 1 Residue: 13( G) Mol: 1 Model: 1 Entry: 1 Residue: 20( C) Mol: 1 Model: 1 Entry: 1 Residue: 14( C) Mol: 1 Model: 1 Entry: 1 Residue: 19( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1jo7_wc.csv Wattos started at: April 20, 2007 11:48:01 AM CDT Wattos stopped at: April 20, 2007 11:48:11 AM CDT Wattos took (#ms): 9516