Read libraries from system resource. Wattos started at: January 19, 2007 10:21:54 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/pdb2fdt.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 12672 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1440 Found number of new bond candidates: 1241 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: 33 Found number of new hydrogen bonds: 33 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 36(C ) 1 1 1 3.168 178.655 5 N2 1(G ) 1 O2 36(C ) 1 1 1 3.119 170.181 5 N1 2(G ) 1 N3 35(C ) 1 1 1 3.177 171.142 5 N2 2(G ) 1 O2 35(C ) 1 1 1 3.106 173.404 5 N3 3(U ) 1 N1 34(A ) 1 1 1 3.190 160.168 5 N3 4(U ) 1 O6 33(G ) 1 1 1 3.246 166.484 5 N1 5(G ) 1 N3 32(C ) 1 1 1 3.112 160.579 5 N2 5(G ) 1 O2 32(C ) 1 1 1 3.085 173.835 5 N3 6(U ) 1 O6 31(G ) 1 1 1 3.214 157.617 5 N1 9(G ) 1 N3 29(C ) 1 1 1 3.143 170.793 5 N2 9(G ) 1 O2 29(C ) 1 1 1 3.099 164.681 5 N3 10(U ) 1 O2 28(U ) 1 1 1 3.278 166.854 5 N4 11(C ) 1 O6 27(G ) 1 1 1 3.150 166.656 5 N1 12(G ) 1 N3 26(C ) 1 1 1 3.173 168.349 5 N2 12(G ) 1 O2 26(C ) 1 1 1 3.120 168.739 5 N4 13(C ) 1 O6 25(G ) 1 1 1 3.111 171.366 5 N3 14(U ) 1 N1 24(A ) 1 1 1 3.126 142.096 5 N3 15(U ) 1 N1 23(A ) 1 1 1 3.165 159.034 5 N6 23(A ) 1 O4 15(U ) 1 1 1 2.506 135.605 5 N6 24(A ) 1 O4 14(U ) 1 1 1 2.452 135.109 5 N1 25(G ) 1 N3 13(C ) 1 1 1 3.186 169.433 5 N2 25(G ) 1 O2 13(C ) 1 1 1 3.125 167.374 5 N4 26(C ) 1 O6 12(G ) 1 1 1 3.096 170.067 5 N1 27(G ) 1 N3 11(C ) 1 1 1 3.146 172.781 5 N2 27(G ) 1 O2 11(C ) 1 1 1 3.072 158.930 5 N3 28(U ) 1 O4 10(U ) 1 1 1 3.113 161.891 5 N4 29(C ) 1 O6 9(G ) 1 1 1 3.108 171.327 5 N1 31(G ) 1 O2 6(U ) 1 1 1 3.088 152.384 5 N4 32(C ) 1 O6 5(G ) 1 1 1 3.128 162.314 5 N1 33(G ) 1 O2 4(U ) 1 1 1 3.168 167.829 5 N6 34(A ) 1 O4 3(U ) 1 1 1 2.474 131.195 5 N4 35(C ) 1 O6 2(G ) 1 1 1 3.111 159.129 5 N4 36(C ) 1 O6 1(G ) 1 1 1 3.109 171.607 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, 2fdt_wc.csv] Trying to match bases to eachother for number of bases: 36 Considering number of hydrogen bonds: 33 Results contains number of sets of co-planar bases: 10 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 36( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 35( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( U) Mol: 1 Model: 1 Entry: 1 Residue: 34( A) Mol: 1 Model: 1 Entry: 1 Residue: 5( G) Mol: 1 Model: 1 Entry: 1 Residue: 32( C) Mol: 1 Model: 1 Entry: 1 Residue: 9( G) Mol: 1 Model: 1 Entry: 1 Residue: 29( C) Mol: 1 Model: 1 Entry: 1 Residue: 11( C) Mol: 1 Model: 1 Entry: 1 Residue: 27( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( G) Mol: 1 Model: 1 Entry: 1 Residue: 26( C) Mol: 1 Model: 1 Entry: 1 Residue: 13( C) Mol: 1 Model: 1 Entry: 1 Residue: 25( G) Mol: 1 Model: 1 Entry: 1 Residue: 14( U) Mol: 1 Model: 1 Entry: 1 Residue: 24( A) Mol: 1 Model: 1 Entry: 1 Residue: 15( U) Mol: 1 Model: 1 Entry: 1 Residue: 23( A) Mol: 1 Model: 1 Entry: 1 Writing results to file: 2fdt_wc.csv Wattos started at: January 19, 2007 10:21:54 AM CST Wattos stopped at: January 19, 2007 10:21:59 AM CST Wattos took (#ms): 5792