ModelCraft

An automated model building pipeline for X-ray crystallography

Getting Started

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

Required Arguments

--hklin FILE
Input reflection data in MTZ format.

--seqin FILE
Input protein sequence in FASTA format.

Optional Arguments

--amplitudes COLS e.g. FP,SIGFP
Column labels for the observed amplitudes.

--convergence-cycles N default: 4
Number of cycles without improvement needed to stop the pipeline automatically. --convergence-tolerance is used to determine whether a cycle gave an improvement.

--convergence-tolerance default: 0.1
R-free difference needed to mark a cycle as an improvement. If the model at the end of a cycle has an R-free that is this much better than the previous best R-free then the cycle is marked as an improvement. --convergence-cycles states how many cycles without improvement are needed to stop automatically.

--cycles N default: 25
Maximum number of pipeline cycles.

--freerflag COL e.g. FreeR_flag
Column label for the free-R flag.

--help
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 /[chain]/[residue]/[atom]:[radius]. E.g. /A/*/*/:2.0 will avoid building within 2Å of the A chain and /*/*/ZN  /:3.0 will avoid building within 3Å of zinc atoms.

--mr-mode CHOICE default: 6
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 --phases.

--mr-model FILE
Input placed molecular replacement model. If input phases are not specified this will be refined.

--no-auto-stop
Run the maximum number of cycles even if the model is not improving.

--phases COLS e.g. PHIB,FOM or HLA,HLB,HLC,HLD
Column labels for input phases as either a phase and figure of merit or Hendrickson-Lattman coefficients.

--semet
Build selenomethionine instead of methionine.

--twinned
Turn on twinned refinement. Only do this if you are sure your data are twinned.

--unbiased
Pass input phases to REFMAC for MLHL refinement.

Developer Arguments

--buccaneer FILE
Path to an alternative buccaneer binary.

Links

References

ModelCraft
Publication in progress
Buccaneer
K Cowtan. Acta Cryst. D62 1002-1011 (2006) DOI
REFMAC
O Kovalevskiy, RA Nicholls, F Long, A Carlon, GN Murshudov. Acta Cryst. D74 215-227 (2018) DOI
Coot
P Emsley, B Lohkamp, WG Scott, K Cowtan. Acta Cryst. D66 486-501 (2010) DOI
Sheetbend
K Cowtan, J Agirre. Acta Cryst. D74 125-131 (2018) DOI
Parrot
K Cowtan. Acta Cryst. D66 470-478 (2010) DOI