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AFITT Usage

While AFITT does not require the use of the command line, it does support limited functionality such as loading files and starting a basic fitting run.

Command Line Interface

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

prompt> afitt --help

will generate the following output:

Help functions:
  afitt --help simple      : Get a list of simple parameters
  afitt --help all         : Get a complete list of parameters
  afitt --help <parameter> : Get detailed help on a parameter
  afitt --help html        : Create an html help file for this program
-load <filename>
Load a file into AFITT. Typical files includes, ligands proteins and density that can be automatically loaded.

File containing a molecule to be fit to density.

File type Extension
SMILES .smi .ism .smi.gz .ism.gz
OEBinary .oeb .oeb.gz
SDF .sdf .mol .sdf.gz .mol.gz
MOL2 .mol2 .mol2.gz
PDB .pdb .ent .pdb.gz .ent.gz
MacroModel .mmod .mmod.gz

Input density grid used to fit ligand.

Grid File type Extension
MTZ .mtz
OpenEye .grd
Grasp .phi
CCP4 .map .ccp4
XPLOR .xplor xplmap
ASCII Grid .agd
-fit

Run a basic fit on the loaded molecules. This is the same as hitting the fit button.

-fitexit

Run a basic fit on the loaded molecules. This is the same as hitting the fit button. Automatically save the output and optionally load it into the viewer selected in the current workflow.