Read libraries from system resource.
Wattos started at: April 20, 2007 11:51:30 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/pdb1n96.ent, PDB]
Read total number of atoms from PDB formatted coordinate list: 5020


Tolerance (0.1 Angstrom suggested)
Doing CalcBond with arguments: [0.1]

Done. Checked number of potential pairs: 620
Found number of new bond candidates: 538


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: 10
Found number of new hydrogen bonds: 10
Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1  Value_2 RefValue    RefSD Type   Minimum  Average  Maximum Under cutoff
N1      2(G  )    1 N3      3(C  )    2      1      1   2.858  170.778                       5
N2      2(G  )    1 O2      3(C  )    2      1      1   2.792  168.729                       5
N4      3(C  )    1 O6      2(G  )    2      1      1   2.838  169.595                       5
N6      6(A  )    1 O4      7(T  )    2      1      1   2.862  168.427                       5
N3      7(T  )    1 N1      6(A  )    2      1      1   2.795  167.602                       5
N1      2(G  )    2 N3      3(C  )    1      1      1   2.851  173.671                       5
N2      2(G  )    2 O2      3(C  )    1      1      1   2.815  173.524                       5
N4      3(C  )    2 O6      2(G  )    1      1      1   2.854  174.967                       5
N6      6(A  )    2 O4      7(T  )    1      1      1   2.828  165.598                       5
N3      7(T  )    2 N1      6(A  )    1      1      1   2.783  169.132                       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, 1n96_wc.csv]
Trying to match bases to eachother for number of bases: 16
Considering number of hydrogen bonds: 10
Results contains number of sets of co-planar bases: 4
Results:
Residue:   2(   G) Mol:   1 Model:   1 Entry:  1
Residue:   3(   C) Mol:   2 Model:   1 Entry:  1

Residue:   3(   C) Mol:   1 Model:   1 Entry:  1
Residue:   2(   G) Mol:   2 Model:   1 Entry:  1

Residue:   6(   A) Mol:   1 Model:   1 Entry:  1
Residue:   7(   T) Mol:   2 Model:   1 Entry:  1

Residue:   7(   T) Mol:   1 Model:   1 Entry:  1
Residue:   6(   A) Mol:   2 Model:   1 Entry:  1

Writing results to file: 1n96_wc.csv


Wattos started at: April 20, 2007 11:51:30 AM CDT
Wattos stopped at: April 20, 2007 11:51:34 AM CDT
Wattos took (#ms): 3563