Read libraries from system resource. Wattos started at: January 19, 2007 10:17:52 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/pdb1mnx.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 17732 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1822 Found number of new bond candidates: 1474 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: 44 Found number of new hydrogen bonds: 44 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 42(C ) 1 1 1 3.029 159.927 5 N2 1(G ) 1 O2 42(C ) 1 1 1 2.854 165.854 5 N1 2(G ) 1 N3 41(C ) 1 1 1 3.021 156.997 5 N2 2(G ) 1 O2 41(C ) 1 1 1 2.936 160.604 5 N1 3(G ) 1 N3 40(C ) 1 1 1 3.022 158.945 5 N2 3(G ) 1 O2 40(C ) 1 1 1 2.913 165.271 5 N3 4(U ) 1 O6 39(G ) 1 1 1 2.905 151.638 5 N2 5(G ) 1 N7 38(A ) 1 1 1 3.037 152.342 5 N6 6(A ) 1 O2 37(U ) 1 1 1 3.082 172.847 5 N4 7(C ) 1 N1 36(A ) 1 1 1 3.130 153.778 5 N3 10(U ) 1 N7 33(A ) 1 1 1 3.018 167.396 5 N4 12(C ) 1 O6 31(G ) 1 1 1 2.948 152.210 5 N3 13(U ) 1 O6 30(G ) 1 1 1 3.069 170.175 5 N1 14(G ) 1 N3 29(C ) 1 1 1 3.056 173.258 5 N2 14(G ) 1 O2 29(C ) 1 1 1 2.916 164.450 5 N3 15(U ) 1 O6 28(G ) 1 1 1 3.060 170.527 5 N6 16(A ) 1 O4 27(U ) 1 1 1 3.016 159.119 5 N1 17(G ) 1 N3 26(C ) 1 1 1 3.023 159.159 5 N2 17(G ) 1 O2 26(C ) 1 1 1 2.940 164.131 5 N1 18(G ) 1 N3 25(C ) 1 1 1 3.020 157.298 5 N2 18(G ) 1 O2 25(C ) 1 1 1 2.919 162.531 5 N4 19(C ) 1 O6 24(G ) 1 1 1 2.862 167.656 5 O2* 20(G ) 1 N7 22(G ) 1 1 1 2.868 175.487 5 N2 20(G ) 1 N7 23(A ) 1 1 1 3.196 164.128 5 O2* 22(G ) 1 O5* 23(A ) 1 1 1 2.972 125.467 5 N6 23(A ) 1 N3 20(G ) 1 1 1 3.054 149.729 5 N1 24(G ) 1 N3 19(C ) 1 1 1 3.039 169.698 5 N2 24(G ) 1 O2 19(C ) 1 1 1 3.014 177.083 5 N4 25(C ) 1 O6 18(G ) 1 1 1 2.951 160.335 5 N4 26(C ) 1 O6 17(G ) 1 1 1 2.969 157.393 5 N3 27(U ) 1 N1 16(A ) 1 1 1 2.902 156.728 5 N1 28(G ) 1 O2 15(U ) 1 1 1 2.851 160.426 5 N2 28(G ) 1 O2 15(U ) 1 1 1 3.066 143.792 5 N4 29(C ) 1 O6 14(G ) 1 1 1 3.016 171.125 5 N1 30(G ) 1 O2 13(U ) 1 1 1 2.868 160.159 5 N1 31(G ) 1 N3 12(C ) 1 1 1 2.981 152.251 5 N2 31(G ) 1 O2 12(C ) 1 1 1 2.891 151.405 5 N6 33(A ) 1 O2 10(U ) 1 1 1 2.907 175.346 5 N3 37(U ) 1 N7 6(A ) 1 1 1 2.963 170.799 5 N6 38(A ) 1 N3 5(G ) 1 1 1 3.136 152.163 5 N1 39(G ) 1 O2 4(U ) 1 1 1 2.915 150.662 5 N4 40(C ) 1 O6 3(G ) 1 1 1 2.962 162.739 5 N4 41(C ) 1 O6 2(G ) 1 1 1 2.951 161.085 5 N4 42(C ) 1 O6 1(G ) 1 1 1 3.006 162.009 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, 1mnx_wc.csv] Trying to match bases to eachother for number of bases: 42 Considering number of hydrogen bonds: 44 Results contains number of sets of co-planar bases: 9 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 42( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 41( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( G) Mol: 1 Model: 1 Entry: 1 Residue: 40( C) Mol: 1 Model: 1 Entry: 1 Residue: 12( C) Mol: 1 Model: 1 Entry: 1 Residue: 31( G) Mol: 1 Model: 1 Entry: 1 Residue: 14( G) Mol: 1 Model: 1 Entry: 1 Residue: 29( C) Mol: 1 Model: 1 Entry: 1 Residue: 16( A) Mol: 1 Model: 1 Entry: 1 Residue: 27( U) Mol: 1 Model: 1 Entry: 1 Residue: 17( G) Mol: 1 Model: 1 Entry: 1 Residue: 26( C) Mol: 1 Model: 1 Entry: 1 Residue: 18( G) Mol: 1 Model: 1 Entry: 1 Residue: 25( C) Mol: 1 Model: 1 Entry: 1 Residue: 19( C) Mol: 1 Model: 1 Entry: 1 Residue: 24( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1mnx_wc.csv Wattos started at: January 19, 2007 10:17:52 AM CST Wattos stopped at: January 19, 2007 10:17:58 AM CST Wattos took (#ms): 5960