5.1 Command Line Interface

Executing aligngrid with no arguments will result in

prompt> aligngrid
          :jGf:
        :jGDDDDf:
      ,fDDDGjLDDDf,            aligngrid
    ,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: 1.0
          .:::.
  ......................       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:
    -grid : Input density grid used to fit against
    -out : The output grid ( in .map(.ccp4) or .grd format )
    -protein : The query protein to be rotated
    -target : The target protein ( to rotate the initial protein into )
For more help type:
  ./aligngrid --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> aligngrid --help

Help functions:
  ./aligngrid --help simple      : Get a list of simple parameters
  ./aligngrid --help all         : Get a complete list of parameters
  ./aligngrid --help defaults    : List the defaults for all parameters
  ./aligngrid --help <parameter> : Get detailed help on a parameter
  ./aligngrid --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> aligngrid --help all

will generate the following output:

Complete parameter list
    File Options
      -grid : Input density grid.
      -out : The output grid ( in .map(.ccp4) or .grd format )
      -protein : The query protein to be rotated
      -target : The target protein ( to rotate the initial protein into )

    Advanced Options
      -outprot : The output aligned protein.
      -padding : When writing a ".grd" file, this indicates the added extents
                 around the protein to output density in Angstroms.
      -scale : Scale the final map spacing. (The default is the minimum initial
               spacing in X, Y or Z)
      -verbose : Triggers copious logging output

    MTZ File parameters
      -Fc : Column to use for Fc.
      -Fdelwt : Column to use for Fdelwt or difference map amplitudes
      -Fobs : Column to use for FObs.
      -Fwt : Column to use for Fwt or regular map amplitudes.
      -Phic : Column to use for Phic.
      -Phidelwt : Column to use for Phdelwt or difference map phases.
      -Phiwt : Column to use for Phwt or regular map phases.
      -autoMTZ : Automatically try to open the mtz file using the DELWT and
                 FDELWT columns from REFMAC5 mtz files.
      -mtype : The map type to use for fitting. Fo-Fc, Fc, 2Fo-Fc, 3Fo-Fc, Fwt,
               Fdelwt...

5.1.1 Required Parameters

-grid: Input density grid. This is the grid that is to be rotated and translated into the new reference frame.
-out: The output grid in any writable format. These include ``.ccp4'', ``.map'' and ``.grd''
-protein: The query protein that corresponds to the input grid.
-target: The target protein that the grid and query protein will be aligned toward.

5.1.2 Advanced Options

-outprot: An optional file to output the query protein after it is translated and rotated into the new reference frame.
-padding: When writing out a ``.grd'' file, this indicates the added extents (in $\AA$ around the protein when outputing the density.
-scale: The final map spacing in $\AA$ . (The default is the minimum spacing in X, Y or Z)
-verbose: Triggers copious logging output.

5.1.3 MTZ File Parameters

-autoMTZ: This flag enables automatically opening mtz files that have been generated from REFMAC5 or standard packages. The appropriate FWT and DELFWT (or FOFCWT and 2FOFCWT) columns are created and used for making the Fwt or Fdelwt maps. [default = true]
-Fobs: Use this MTZ column as the observed amplitude column. [default = F]
-Fc: Use this MTZ column as the calculated amplitude column. Note, to load arbitrary columns, you can use the ``-Fc'' and ``-Phic'' columns and the ``Fc'' maptype. [default = FC]
-Phic: Use this MTZ column as the calculated phase column [default = PHIC]
-Fdelwt: Column to use for Fdelwt or difference map amplitudes.
-Fwt: Column to use for Fwt or regular map amplitudes.
-Phic: Column to use for Phic.
-Phidelwt: Column to use for Phdelwt or difference map phases.
-Phiwt: Column to use for Phwt or regular map phases.
-mtype: This argument indicates what type of map will be used for the ligand placement. Available options are Fc, 2Fo-Fc, 3Fo-Fc, 5Fo-3Fc, 2Fo-Fc (SigmaA), Fo-Fc (SigmaA), Fwt, Fdelwt [default = 2Fo-Fc]

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