Read libraries from system resource. Wattos started at: April 20, 2007 11:53:31 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/pdb1r7w.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 21760 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1398 Found number of new bond candidates: 1171 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: 31 Found number of new hydrogen bonds: 31 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 34(C ) 1 1 1 3.033 162.000 5 N2 1(G ) 1 O2 34(C ) 1 1 1 2.940 169.223 5 N1 2(G ) 1 N3 33(C ) 1 1 1 3.025 168.351 5 N2 2(G ) 1 O2 33(C ) 1 1 1 3.107 162.382 5 N1 4(G ) 1 N3 31(C ) 1 1 1 3.034 167.023 5 N2 4(G ) 1 O2 31(C ) 1 1 1 2.767 158.184 5 N1 5(G ) 1 N3 30(C ) 1 1 1 3.087 169.444 5 N2 5(G ) 1 O2 30(C ) 1 1 1 3.154 177.460 5 N6 6(A ) 1 O4 29(U ) 1 1 1 3.120 167.388 5 N4 14(C ) 1 O6 27(G ) 1 1 1 2.848 167.617 5 N6 15(A ) 1 O4 26(U ) 1 1 1 2.872 165.093 5 N4 16(C ) 1 O6 25(G ) 1 1 1 2.945 152.067 5 N1 17(G ) 1 N3 24(C ) 1 1 1 2.942 167.345 5 N2 17(G ) 1 O2 24(C ) 1 1 1 2.865 153.522 5 N1 18(G ) 1 N3 23(C ) 1 1 1 3.033 169.684 5 N2 18(G ) 1 O2 23(C ) 1 1 1 3.079 166.405 5 O2* 19(G ) 1 N7 21(G ) 1 1 1 3.006 152.183 5 N2 19(G ) 1 N7 22(A ) 1 1 1 2.837 126.709 5 N4 23(C ) 1 O6 18(G ) 1 1 1 2.855 168.101 5 N4 24(C ) 1 O6 17(G ) 1 1 1 2.942 164.782 5 N1 25(G ) 1 N3 16(C ) 1 1 1 2.851 147.859 5 N2 25(G ) 1 O2 16(C ) 1 1 1 2.858 126.061 5 N3 26(U ) 1 N1 15(A ) 1 1 1 2.880 143.315 5 N1 27(G ) 1 N3 14(C ) 1 1 1 3.005 165.514 5 N1 28(G ) 1 N3 7(C ) 1 1 1 2.957 165.216 5 N2 28(G ) 1 O2 7(C ) 1 1 1 2.810 167.187 5 N3 29(U ) 1 N1 6(A ) 1 1 1 2.900 162.879 5 N4 30(C ) 1 O6 5(G ) 1 1 1 2.881 164.202 5 N4 31(C ) 1 O6 4(G ) 1 1 1 3.142 162.318 5 N3 32(U ) 1 N1 3(A ) 1 1 1 2.869 169.128 5 N4 33(C ) 1 O6 2(G ) 1 1 1 2.756 158.560 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, 1r7w_wc.csv] Trying to match bases to eachother for number of bases: 34 Considering number of hydrogen bonds: 31 Results contains number of sets of co-planar bases: 11 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 34( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 33( C) Mol: 1 Model: 1 Entry: 1 Residue: 4( G) Mol: 1 Model: 1 Entry: 1 Residue: 31( C) Mol: 1 Model: 1 Entry: 1 Residue: 5( G) Mol: 1 Model: 1 Entry: 1 Residue: 30( C) Mol: 1 Model: 1 Entry: 1 Residue: 6( A) Mol: 1 Model: 1 Entry: 1 Residue: 29( U) Mol: 1 Model: 1 Entry: 1 Residue: 7( C) Mol: 1 Model: 1 Entry: 1 Residue: 28( G) Mol: 1 Model: 1 Entry: 1 Residue: 14( C) Mol: 1 Model: 1 Entry: 1 Residue: 27( G) Mol: 1 Model: 1 Entry: 1 Residue: 15( A) Mol: 1 Model: 1 Entry: 1 Residue: 26( U) Mol: 1 Model: 1 Entry: 1 Residue: 16( C) Mol: 1 Model: 1 Entry: 1 Residue: 25( G) Mol: 1 Model: 1 Entry: 1 Residue: 17( G) Mol: 1 Model: 1 Entry: 1 Residue: 24( C) Mol: 1 Model: 1 Entry: 1 Residue: 18( G) Mol: 1 Model: 1 Entry: 1 Residue: 23( C) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1r7w_wc.csv Wattos started at: April 20, 2007 11:53:31 AM CDT Wattos stopped at: April 20, 2007 11:53:37 AM CDT Wattos took (#ms): 6403