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

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

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

--colin-hl COLS e.g. HLA,HLB,HLC,HLD
Column labels for input phases as Hendrickson-Lattman coefficients.

--colin-phifom COLS e.g. PHIB,FOM
Column labels for input phases as a phase and figure of merit.

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

--fix-side-chains
Once R-work drops below 30%, fix side chains with low correctness scores at the end of each cycle. The fix uses Coot to delete the side chain, refine the residue and its neighbours, re-add and auto-fit the side chain, then refine the residue with its neighbours again. The resulting model is only accepted if R-free improves. This step is very slow so is not used by default.

--free-r-flag N default: 0
Flag that identifies the free reflections.

--help
Show an automatically generated help message.

--keep-intermediate-files
Don't delete intermediate files.

--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 --colin-hl or --colin-phifom.

--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.

--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
Parrot
K Cowtan. Acta Cryst. D66 470-478 (2010) DOI