Read libraries from system resource. Wattos started at: April 20, 2007 11:52:52 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/pdb1pqq.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 17199 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1017 Found number of new bond candidates: 878 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: 35 Found number of new hydrogen bonds: 35 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N4 1(C ) 1 O6 11(G ) 2 1 1 2.951 174.865 5 N1 2(G ) 1 N3 10(C ) 2 1 1 2.950 171.560 5 N2 2(G ) 1 O2 10(C ) 2 1 1 2.836 174.472 5 N4 3(C ) 1 O6 9(G ) 2 1 1 2.901 173.651 5 N3 4(T ) 1 N1 8(A ) 2 1 1 2.903 166.507 5 N6 5(A ) 1 O4 7(T ) 2 1 1 2.885 173.353 5 N6 6(A ) 1 O4 6(T ) 2 1 1 2.864 176.431 5 N4 7(C ) 1 O6 5(G ) 2 1 1 2.845 172.292 5 N6 8(A ) 1 O4 4(T ) 2 1 1 3.104 178.688 5 N1 9(G ) 1 O2 3(C ) 2 1 1 3.174 136.145 5 N1 9(G ) 1 N3 3(C ) 2 1 1 2.946 159.952 5 N2 9(G ) 1 O2 3(C ) 2 1 1 2.801 156.490 5 N1 10(G ) 1 N3 2(C ) 2 1 1 2.933 171.006 5 N2 10(G ) 1 O2 2(C ) 2 1 1 2.864 169.171 5 N4 11(C ) 1 O6 1(G ) 2 1 1 2.925 176.255 5 N1 1(G ) 2 N3 11(C ) 1 1 1 2.954 171.287 5 N2 1(G ) 2 O2 11(C ) 1 1 1 2.835 172.121 5 N4 2(C ) 2 O6 10(G ) 1 1 1 2.896 173.171 5 N4 3(C ) 2 O6 9(G ) 1 1 1 2.931 166.836 5 N3 4(T ) 2 N1 8(A ) 1 1 1 2.909 170.052 5 N1 5(G ) 2 N3 7(C ) 1 1 1 2.894 171.438 5 N2 5(G ) 2 O2 7(C ) 1 1 1 2.836 175.364 5 N2 5(G ) 2 N2 1(CYE) 3 1 1 3.100 168.619 5 N3 6(T ) 2 N1 6(A ) 1 1 1 2.962 170.118 5 N3 7(T ) 2 N1 5(A ) 1 1 1 2.878 170.343 5 N6 8(A ) 2 O4 4(T ) 1 1 1 3.068 168.492 5 N1 9(G ) 2 N3 3(C ) 1 1 1 2.937 165.160 5 N2 9(G ) 2 O2 3(C ) 1 1 1 2.840 169.635 5 N4 10(C ) 2 O6 2(G ) 1 1 1 2.911 177.900 5 N1 11(G ) 2 N3 1(C ) 1 1 1 2.931 168.420 5 N2 11(G ) 2 O2 1(C ) 1 1 1 2.827 171.640 5 N6 1(CYE) 3 O2 7(T ) 2 1 1 3.020 155.148 5 N4 1(CYE) 3 O2 6(T ) 2 1 1 2.800 152.440 5 N15 1(CYE) 3 N3 5(G ) 2 1 1 2.953 151.524 5 N1 1(CYE) 3 N3 8(A ) 1 1 1 3.019 135.961 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, 1pqq_wc.csv] Trying to match bases to eachother for number of bases: 22 Considering number of hydrogen bonds: 35 Results contains number of sets of co-planar bases: 11 Results: Residue: 1( C) Mol: 1 Model: 1 Entry: 1 Residue: 11( G) Mol: 2 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 10( C) Mol: 2 Model: 1 Entry: 1 Residue: 3( C) Mol: 1 Model: 1 Entry: 1 Residue: 9( G) Mol: 2 Model: 1 Entry: 1 Residue: 4( T) Mol: 1 Model: 1 Entry: 1 Residue: 8( A) Mol: 2 Model: 1 Entry: 1 Residue: 5( A) Mol: 1 Model: 1 Entry: 1 Residue: 7( T) Mol: 2 Model: 1 Entry: 1 Residue: 6( A) Mol: 1 Model: 1 Entry: 1 Residue: 6( T) Mol: 2 Model: 1 Entry: 1 Residue: 7( C) Mol: 1 Model: 1 Entry: 1 Residue: 5( G) Mol: 2 Model: 1 Entry: 1 Residue: 8( A) Mol: 1 Model: 1 Entry: 1 Residue: 4( T) Mol: 2 Model: 1 Entry: 1 Residue: 9( G) Mol: 1 Model: 1 Entry: 1 Residue: 3( C) Mol: 2 Model: 1 Entry: 1 Residue: 10( G) Mol: 1 Model: 1 Entry: 1 Residue: 2( C) Mol: 2 Model: 1 Entry: 1 Residue: 11( C) Mol: 1 Model: 1 Entry: 1 Residue: 1( G) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1pqq_wc.csv Wattos started at: April 20, 2007 11:52:52 AM CDT Wattos stopped at: April 20, 2007 11:52:59 AM CDT Wattos took (#ms): 6844