ModelCraft can be installed using pip.
python3 -m pip install --user modelcraft
It also requires an installation of CCP4. The CCP4 environment needs to be set up for the pipeline to work. The simplest execution requires only a reflection data file in MTZ format and a sequence file in FASTA format.
modelcraft --hklin reflections.mtz --seqin sequence.fasta
Input reflection data in MTZ format.
Input protein sequence in FASTA format.
--amplitudes COLS e.g.
Column labels for the observed amplitudes.
--cycles N default:
Maximum number of pipeline cycles.
--freerflag COL e.g.
Column label for the free-R flag.
Show an automatically generated help message.
--known-structure SELECTION [SELECTION ...]
Known structure selections from the input coordinates. Buccaneer will avoid building into these selections and they will be copied into the output coordinates. Multiple selections can be specified. The format is
will avoid building within 2Å of the A chain
will avoid building within 3Å of zinc atoms.
--mr-mode CHOICE default:
Determine how the molecular replacement model is used:
1 - Phasing
2 - Phasing, placing/naming chains
3 - Phasing, placing/naming chains, copy every residue
4 - Phasing, placing/naming chains, copy every filtered residue
5 - Phasing, placing/naming chains, copy every 3rd residue
6 - Phasing, placing/naming chains, copy every 3rd filtered residue
The MR model will not be used for phasing if input phases are provided using
Input placed molecular replacement model. If input phases are not specified this will be refined.
Run the maximum number of cycles even if the model is not improving.
Column labels for input phases as either a phase and figure of merit or Hendrickson-Lattman coefficients.
Build selenomethionine instead of methionine.
Turn on twinned refinement. Only do this if you are sure your data are twinned.
Pass input phases to REFMAC for MLHL refinement.
Path to an alternative buccaneer binary.