ModelCraft

Command Line Interface

Installation

ModelCraft is distributed with CCP4 (version 8 onwards) and can be run from the CCP4 command line, but if a newer version of ModelCraft is required it can also be installed using pip for Python 3.7 or newer, e.g.

python3 -m pip install --user modelcraft

Refer to the pip documentation if pip is not installed. In order to run ModelCraft, the CCP4 environment needs to be set up so that programs (such as Buccaneer and Refmac) can be called from the command line. For building into cryo-EM maps, the CCP-EM environment also needs to be sourced.

Usage

The first argument must be either xray or em for X-ray crystallography or cryo-EM. The simplest execution for X-ray crystallography requires only a description of the asymmetric unit contents (see the next section) and a reflection data file in MTZ format (with observations, a free-R flag and starting phases).

modelcraft xray --contents contents.json --data data.mtz

Alternatively, a model can be provided (in PDB, mmCIF or mmJSON format), which will be refined and used as a starting point instead of starting from phases in the data file.

modelcraft xray --contents contents.json --data data.mtz --model model.cif

For cryo-EM, either two halfmaps or a single map must be provided along with a resolution.

modelcraft em --contents contents.json --map half1.mrc half2.mrc --resolution 2.5
modelcraft em --contents contents.json --map map.mrc --resolution 2.5

The command line documentation has more detailed information on individual arguments.

modelcraft xray --help
modelcraft em --help

ASU Contents Description

A description of the expected contents of the asymmetric unit must be provided as either a FASTA sequence file or a JSON file using the --contents argument. A sequence file is simpler, but the JSON format has the following advantages:

Number of copies and stoichiometry can be specified for a more accurate calculation of the solvent fraction.
Carbohydrates, ligands and buffers may be specified in addition to protein, RNA and DNA.
Molecule types do not need to be guessed from sequences (which may be ambiguous).

In order to create a JSON file it may be helpful to start from the contents for an existing PDB entry. The modelcraft-contents script creates a contents JSON file for a released PDB entry.

An example JSON file is shown below:

{
    "copies": 2,
    "proteins": [
        {
            "sequence": "LPGECSVNVIPKMNLDKAKFFSGTWYETHYLDMDPQATEKFCFSFAPRESGGTVMEALYHFNVDSKV",
            "stoichiometry": 1,
            "modifications": ["M->MSE"]
        },
        {
            "sequence": "GGG"
        }
    ],
    "rnas": [
        {
            "sequence": "GGUAACUGUUACAGUUACC",
            "stoichiometry": 2,
            "modifications": ["1->GTP", "19->CCC"]
        }
    ],
    "dnas": [],
    "carbs": [
        { "codes": { "NAG": 2 }, "stoichiometry": 1 },
        { "codes": { "MAN": 1, "NAG": 2 }, "stoichiometry": 1 }
    ],
    "ligands": [
        { "code": "HEM", "stoichiometry": 1 }
    ],
    "buffers": ["GOL", "NA", "CL"]
}

The file has a list of proteins, rnas, dnas, carbs, ligands, and buffers that are in the crystal. The only mandatory items are that each protein, RNA or DNA chain must have a sequence, each carbohydrate must have a dictionary of codes to specify the number of each sugar, and each ligand must have a single code.

Each component (other than buffers) has a stoichiometry parameter to specify the stoichiometry. In the example above there are 2 RNA chains for each protein chain. If the stoichiometry is not specified it is assumed to be 1. There is also a copies parameter for the whole file to specify how many copies of the contents are in the asymmetric unit. If this value is not known the most likely number will be estimated. The modelcraft-copies script can be used to view the solvent fraction and probability for each number of copies given a contents file and an MTZ file. It is assumed that the number of ordered buffer molecules is unknown so they are not included in the solvent calculation.

Finally, protein, RNA and DNA chains may have a list of modifications, e.g. M->MSE to specify that all methionine residues are actually selenomethionine or 1->GTP to specify that the residue 1 is guanosine triphosphate.

Note: ModelCraft does not yet build carbohydrates, ligands, or modified residues (other than selenomethionine derivatives). However, this is planned for the future and inclusion of these components in the contents allows for more accurate calculation of the solvent fraction during Parrot density modification in the X-ray pipeline.

ModelCraft

Automated model building of proteins and nucleic acids in X-ray crystallography and cryo-EM

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