Read libraries from system resource. Wattos started at: April 20, 2007 11:50:20 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/pdb1lmv.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 6060 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 804 Found number of new bond candidates: 652 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: 22 Found number of new hydrogen bonds: 22 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 10(C ) 2 1 1 2.993 163.575 5 N2 1(G ) 1 O2 10(C ) 2 1 1 2.849 170.384 5 N1 2(G ) 1 N3 9(C ) 2 1 1 3.052 168.450 5 N2 2(G ) 1 O2 9(C ) 2 1 1 2.894 163.416 5 N3 3(U ) 1 N1 8(A ) 2 1 1 3.013 159.811 5 N1 4(G ) 1 N3 7(C ) 2 1 1 2.954 168.292 5 N2 4(G ) 1 O2 7(C ) 2 1 1 2.853 162.790 5 N3 5(U ) 1 N1 6(A ) 2 1 1 2.949 161.268 5 N1 7(G ) 1 N3 3(C ) 2 1 1 2.984 167.732 5 N2 7(G ) 1 O2 3(C ) 2 1 1 3.049 154.691 5 N3 8(U ) 1 N1 2(A ) 2 1 1 2.959 158.584 5 N6 9(A ) 1 O4 8(U ) 1 1 1 2.820 104.781 5 N6 9(A ) 1 O4 1(U ) 2 1 1 3.069 167.447 5 N3 1(U ) 2 N1 9(A ) 1 1 1 2.883 171.385 5 N6 2(A ) 2 O4 8(U ) 1 1 1 2.913 162.606 5 N4 3(C ) 2 O6 7(G ) 1 1 1 2.895 163.956 5 O2* 5(A ) 2 O4* 6(A ) 2 1 1 2.915 162.100 5 N4 7(C ) 2 O6 4(G ) 1 1 1 3.066 149.682 5 N6 8(A ) 2 O4 3(U ) 1 1 1 2.860 155.802 5 O2* 9(C ) 2 O4* 10(C ) 2 1 1 2.849 153.124 5 N4 9(C ) 2 O6 2(G ) 1 1 1 3.088 164.464 5 N4 10(C ) 2 O6 1(G ) 1 1 1 2.990 157.892 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, 1lmv_wc.csv] Trying to match bases to eachother for number of bases: 19 Considering number of hydrogen bonds: 22 Results contains number of sets of co-planar bases: 7 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 10( C) Mol: 2 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 9( C) Mol: 2 Model: 1 Entry: 1 Residue: 3( U) Mol: 1 Model: 1 Entry: 1 Residue: 8( A) Mol: 2 Model: 1 Entry: 1 Residue: 4( G) Mol: 1 Model: 1 Entry: 1 Residue: 7( C) Mol: 2 Model: 1 Entry: 1 Residue: 7( G) Mol: 1 Model: 1 Entry: 1 Residue: 3( C) Mol: 2 Model: 1 Entry: 1 Residue: 8( U) Mol: 1 Model: 1 Entry: 1 Residue: 2( A) Mol: 2 Model: 1 Entry: 1 Residue: 9( A) Mol: 1 Model: 1 Entry: 1 Residue: 1( U) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1lmv_wc.csv Wattos started at: April 20, 2007 11:50:20 AM CDT Wattos stopped at: April 20, 2007 11:50:25 AM CDT Wattos took (#ms): 4546