Read libraries from system resource. Wattos started at: April 20, 2007 11:48:13 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/pdb1jrv.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 13770 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1125 Found number of new bond candidates: 990 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: 31 Found number of new hydrogen bonds: 31 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 O2 12(C ) 2 1 1 3.057 143.812 5 N1 1(G ) 1 N3 12(C ) 2 1 1 3.013 151.041 5 N2 1(G ) 1 O2 12(C ) 2 1 1 2.914 152.614 5 N4 2(C ) 1 O6 11(G ) 2 1 1 2.953 169.141 5 N6 3(A ) 1 O4 10(T ) 2 1 1 3.263 155.612 5 N3 4(T ) 1 N1 9(A ) 2 1 1 2.779 142.433 5 N4 5(C ) 1 O6 8(G ) 2 1 1 3.030 153.137 5 N1 6(G ) 1 N3 7(C ) 2 1 1 2.950 162.054 5 N2 6(G ) 1 O2 7(C ) 2 1 1 2.962 154.726 5 N1 12(G ) 1 N3 6(C ) 2 1 1 2.989 171.465 5 N2 12(G ) 1 O2 6(C ) 2 1 1 2.973 167.480 5 N4 13(C ) 1 N6 4(A ) 2 1 1 3.247 118.472 5 N4 13(C ) 1 O6 5(G ) 2 1 1 2.958 154.688 5 N3 14(T ) 1 N1 4(A ) 2 1 1 2.946 168.577 5 N6 15(A ) 1 O4 3(T ) 2 1 1 3.037 162.677 5 N4 16(C ) 1 O6 2(G ) 2 1 1 2.988 169.653 5 N1 2(G ) 2 N3 16(C ) 1 1 1 2.976 172.878 5 N2 2(G ) 2 O2 16(C ) 1 1 1 2.883 174.047 5 N3 3(T ) 2 N1 15(A ) 1 1 1 2.855 159.395 5 N6 4(A ) 2 O4 14(T ) 1 1 1 2.881 152.301 5 N1 5(G ) 2 N3 13(C ) 1 1 1 2.958 157.634 5 N2 5(G ) 2 O2 13(C ) 1 1 1 2.863 156.308 5 N4 6(C ) 2 O6 12(G ) 1 1 1 2.921 162.875 5 N4 7(C ) 2 O6 6(G ) 1 1 1 2.892 173.955 5 N1 8(G ) 2 N3 5(C ) 1 1 1 3.064 164.225 5 N2 8(G ) 2 O2 5(C ) 1 1 1 2.983 155.077 5 N6 9(A ) 2 O4 4(T ) 1 1 1 3.059 173.222 5 N3 10(T ) 2 N1 3(A ) 1 1 1 2.802 163.064 5 N1 11(G ) 2 N3 2(C ) 1 1 1 2.973 168.814 5 N2 11(G ) 2 O2 2(C ) 1 1 1 2.898 169.484 5 N4 12(C ) 2 O6 1(G ) 1 1 1 2.998 148.814 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, 1jrv_wc.csv] Trying to match bases to eachother for number of bases: 29 Considering number of hydrogen bonds: 31 Results contains number of sets of co-planar bases: 11 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( C) Mol: 2 Model: 1 Entry: 1 Residue: 2( C) Mol: 1 Model: 1 Entry: 1 Residue: 11( G) Mol: 2 Model: 1 Entry: 1 Residue: 3( A) Mol: 1 Model: 1 Entry: 1 Residue: 10( T) Mol: 2 Model: 1 Entry: 1 Residue: 4( T) Mol: 1 Model: 1 Entry: 1 Residue: 9( A) Mol: 2 Model: 1 Entry: 1 Residue: 5( C) Mol: 1 Model: 1 Entry: 1 Residue: 8( G) Mol: 2 Model: 1 Entry: 1 Residue: 6( G) Mol: 1 Model: 1 Entry: 1 Residue: 7( C) Mol: 2 Model: 1 Entry: 1 Residue: 12( G) Mol: 1 Model: 1 Entry: 1 Residue: 6( C) Mol: 2 Model: 1 Entry: 1 Residue: 13( C) Mol: 1 Model: 1 Entry: 1 Residue: 5( G) Mol: 2 Model: 1 Entry: 1 Residue: 14( T) Mol: 1 Model: 1 Entry: 1 Residue: 4( A) Mol: 2 Model: 1 Entry: 1 Residue: 15( A) Mol: 1 Model: 1 Entry: 1 Residue: 3( T) Mol: 2 Model: 1 Entry: 1 Residue: 16( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1jrv_wc.csv Wattos started at: April 20, 2007 11:48:13 AM CDT Wattos stopped at: April 20, 2007 11:48:19 AM CDT Wattos took (#ms): 5626