4.1 Command Line Interface

Executing writedict with no arguments will result in

prompt> writedict
          :jGf:
        :jGDDDDf:
      ,fDDDGjLDDDf,           writedict
    ,fDDLt:   :iLDDL;
  ;fDLt:         :tfDG;
,jft:   ,ijfffji,   :iff
     .jGDDDDDDDDDGt.
    ;GDDGt:''':tDDDG,
   .DDDG:       :GDDG.
   ;DDDj         tDDDi
   ,DDDf         fDDD,         Copyright (c) 2008
    LDDDt.     .fDDDj          OpenEye Scientific Software, Inc.
    .tDDDDfjtjfDDDGt
      :ifGDDDDDGfi.            Version: 1.1
          .:::.
  ......................       OEChem version: 1.6.0 20080514
  DDDDDDDDDDDDDDDDDDDDDD       Platform: osx-10.5-g++4.0-x86
  DDDDDDDDDDDDDDDDDDDDDD



  Licensed for the exclusive use of OpenEye Scientific Software.
  Licensed for use Worldwide


No argument specified on the command line
Required parameters:
    -in : Input protein used to prepare for refinement
    -out : Ouput prefix for generating the output protein (<prefix>.pdb) and dictionary (<prefix>.cif)
For more help type:
  ./writedict --help

For the rest of this document, the OpenEye banner will be omitted.

A description of the command line interface can be obtained by executing writedict with the -help option.

prompt> writedict --help

Help functions:
  ./writedict --help simple      : Get a list of simple parameters
  ./writedict --help all         : Get a complete list of parameters
  ./writedict --help defaults    : List the defaults for all parameters
  ./writedict --help <parameter> : Get detailed help on a parameter
  ./writedict --help html        : Create an html help file for this program

If you desire to see all of the command-line options use -help all.

prompt> writedict --help all

will generate the following output:

Complete parameter list
    File Options
      -in : Input protein used to prepare for refinement
      -out : Ouput prefix for generating the output protein (<prefix>.pdb) and
             dictionary (<prefix>.cif)

      Output Options
        -assignCCP4 : Assigns ccp4 types to atoms [default true]
        -includeRotors : Include rotors [default true]
        -suppressH : Suppress hydrogens [default false]
        -type : 0 for REFMAC 1 for XPLOR [default 0 (REFMAC)]
        -planarAniline : force planar contraints for aniline nitrogens  [default false].
        -writeFullDict : Write out entries for all residues. Note that if this
                         option is false covalent links are found, only linked residues
                         are written along with the ligand. Otherwise all residues
                         are written. [default false]

4.1.1 Required Parameters

-in: File containing one or more ligand or proteins to generate refinement dictionaries from. File format types are discussed in section 3.1.2.
-out: This specifies a prefix for ouputting the refinement dictionary (.cif) and a pdb file. The pdb file is always output and should be used for purposes of refinement since writedict sometimes corrects faulty hydrogen atom names and will include LINK records in the pdb if covalent bonds are detected. File formats are discussed in section .

4.1.2 Output Options

-assignCCP4: If true then CCP4 atom types will be assigned to the output pdb file. This is true by default.
-includeRotors: Set to true if the output should include rotor torsion terms. If this is set to false, refinement programs will not be able to modify any rotors. This is true by default.
-supressH: If true, no hydrogens are output. This is false by default.
-type: set this to 0 for refmac5 refinement dictionaries or 1 for CNS/CNX (XPLOR). By default refmac5 dictionaries are generated.
-mmff94s: Use the mmff94s variant of the MMFF94 forcefield. This forcefield emulates time-averages structures observed in crystallographic and other structure determination methods. [default = false]
-writeFullDict: If true then all refinement dictionaries are created for all residues. If false only residues that are unknown or covalently bound to a ligand are output. Setting this to true can confuse refmac5. The default is false.

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