Read libraries from system resource. Wattos started at: April 20, 2007 11:53:07 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/pdb1qe7.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 5670 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 695 Found number of new bond candidates: 609 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: 25 Found number of new hydrogen bonds: 25 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff O5* 1(A ) 1 O2P 2(G ) 1 1 1 2.685 170.842 5 N6 1(A ) 1 O6 2(G ) 1 1 1 3.035 101.100 5 N6 1(A ) 1 O4 18(T ) 1 1 1 2.949 164.451 5 N1 2(G ) 1 O2 17(C ) 1 1 1 3.285 134.786 5 N1 2(G ) 1 N3 17(C ) 1 1 1 2.852 166.190 5 N2 2(G ) 1 O2 17(C ) 1 1 1 2.821 165.534 5 N1 3(G ) 1 N3 16(C ) 1 1 1 2.857 170.473 5 N2 3(G ) 1 O2 16(C ) 1 1 1 2.816 163.401 5 N6 4(A ) 1 O4 15(T ) 1 1 1 2.845 170.798 5 N3 5(T ) 1 N1 14(A ) 1 1 1 2.814 165.875 5 N4 6(C ) 1 O6 13(G ) 1 1 1 2.854 175.725 5 N4 7(C ) 1 O6 12(G ) 1 1 1 2.813 169.956 5 N3 8(T ) 1 O4 10(T ) 1 1 1 2.748 149.088 5 N1 12(G ) 1 N3 7(C ) 1 1 1 2.869 170.684 5 N2 12(G ) 1 O2 7(C ) 1 1 1 2.859 177.346 5 N2 12(G ) 1 O4* 13(G ) 1 1 1 3.141 130.749 5 N1 13(G ) 1 O2 6(C ) 1 1 1 3.238 133.975 5 N1 13(G ) 1 N3 6(C ) 1 1 1 2.862 166.073 5 N2 13(G ) 1 O2 6(C ) 1 1 1 2.792 162.715 5 N2 13(G ) 1 O4* 14(A ) 1 1 1 3.200 128.229 5 N6 14(A ) 1 O4 5(T ) 1 1 1 2.863 170.331 5 N3 15(T ) 1 N1 4(A ) 1 1 1 2.826 174.157 5 N4 16(C ) 1 O6 3(G ) 1 1 1 2.829 169.412 5 N4 17(C ) 1 O6 2(G ) 1 1 1 2.796 161.944 5 N3 18(T ) 1 N1 1(A ) 1 1 1 2.794 167.763 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, 1qe7_wc.csv] Trying to match bases to eachother for number of bases: 18 Considering number of hydrogen bonds: 25 Results contains number of sets of co-planar bases: 7 Results: Residue: 1( A) Mol: 1 Model: 1 Entry: 1 Residue: 18( T) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 17( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( G) Mol: 1 Model: 1 Entry: 1 Residue: 16( C) Mol: 1 Model: 1 Entry: 1 Residue: 4( A) Mol: 1 Model: 1 Entry: 1 Residue: 15( T) Mol: 1 Model: 1 Entry: 1 Residue: 5( T) Mol: 1 Model: 1 Entry: 1 Residue: 14( A) Mol: 1 Model: 1 Entry: 1 Residue: 6( C) Mol: 1 Model: 1 Entry: 1 Residue: 13( G) Mol: 1 Model: 1 Entry: 1 Residue: 7( C) Mol: 1 Model: 1 Entry: 1 Residue: 12( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1qe7_wc.csv Wattos started at: April 20, 2007 11:53:07 AM CDT Wattos stopped at: April 20, 2007 11:53:12 AM CDT Wattos took (#ms): 4288