Setting up the JSON project file

Note

You can find a ready-to-use JSON file named

elongator.json

in the tutorial directory and skip directly to the next step.

Create Xlink Analyzer project

Here is the instruction how to create the JSON file from scratch.

First, you need to create XlinkAnalyzer project file for your complex

Note

XlinkAnalyzer is used here as a graphical interface for input preparation in Assembline.

Does not matter if you do not have crosslinks - we use XlinkAnalyzer to prepare the input file for modeling.

Open Xlink Analyzer window:
In the Xlink Analyzer project Setup tab, define subunits using the menu on the left. For each subunit, enter the name, the chain ID or comma-separated multiple IDs, define the color, and click Add button.

Set up the chain IDs as you want them in the final models, they do not have to correspond to chain IDs in your input PDB files.

The result should look like this:
Click on the Domains button and define domains of Elp1 in the window that opens - they will be used later for adding restraints:

Close the Domains window.
Load sequence data using the panel on the right in the Setup tab.

For this, prepare a file with sequences of all proteins in a single file in FASTA format

Here, use the elp_sequences.fasta file provided in the tutorial materials.

Upload the file using the Browse button, enter a name (e.g. “sequences”) and select “sequence” type in the drop down menu.

Click Add button.

Map the sequence names to names of subunits by clicking the Map button and selecting the subunits in a window that opens. After the mapping, click on the “check” button that turns red.

The result should look like this:

Load crosslink data using the same panel on the left in the Setup tab.

The crosslink files need to be provided in Xlink Analyzer or xQuest format.

Here, the files in xQuest format have been prepared in the tutorial materials:
xlinks/
    DSS/
        inter_run3_190412.clean_strict.csv
        intra_run3_190412.clean_strict.csv
        loop_run3_190412.clean_strict.csv
        mono_run3_190412.clean_strict.csv
        sg1-inter.clean_strict.csv
        sg1-intra.clean_strict.csv
        sg1-loop.clean_strict.csv
        sg2-3-inter.clean_strict.csv
        sg2-3-intra.clean_strict.csv
        sg2-3-loop.clean_strict.csv
        sg2-3-mono.clean_strict.csv
    DSG/
        inter_dsg.clean_strict.csv
        inter_dsg_repeat.clean_strict.csv
        intra_dsg.clean_strict.csv
        intra_dsg_repeat.clean_strict.csv
        loop_dsg.clean_strict.csv
        loop_dsg_repeat.clean_strict.csv
        mono_dsg.clean_strict.csv
        mono_dsg_repeat.clean_strict.csv
The files contain crosslinking results for two crosslinkers (DSS and DSG) in multiple files (multiple runs, inter/intra/loop/mono crosslinks in different files)

Name the first dataset “DSS” click Browse button and select all CSV files from the DSS directory. Set type to xquest or XlinkAnalyzer. Repeat for DSG.

Map crosslinked protein names to the subunit names using the Map button

After the operations above you should end up with sth like this:

Save the JSON file under a name like
```
xla_project.json
```
And make a copy that you will modify for modeling
```
cp xla_project.json elongator.json
```

Add modeling information to the project file

Open elongator.json in a text editor

Note

The project file is in so-called JSON format

While it may look difficult to edit at the first time, it is actually quite OK with a proper editor (and a bit of practice ;-)

We recommend to use a good editor such as:

SublimeText

Atom

At this point, the JSON has the following format:
{
    "data": [
        {
            "some xlink definition 1"
        },
        {
            "some xlink definition 2"
        },
        {
            "sequence file definition"
        }
    ],
    "subunits": [
            "subunit definitions"
    ],
    "xlinkanalyzerVersion": "..."
}

Add symmetry

First, specify the series of symmetry related molecules. Here, each of the three subunits is in two symmetrical copies, so we add series as below:

{
    "series": [
        {
            "name": "2fold",
            "subunit": "Elp1",
            "mode": "input",
            "cell_count": 2,
            "tr3d": "2fold",
            "inipos": "input"
        },
        {
            "name": "2fold",
            "subunit": "Elp2",
            "mode": "auto",
            "cell_count": 2,
            "tr3d": "2fold",
            "inipos": "input"
        },
        {
            "name": "2fold",
            "subunit": "Elp3",
            "mode": "auto",
            "cell_count": 2,
            "tr3d": "2fold",
            "inipos": "input"
        }
    ]
    "data": [
        {
            "some xlink definition 1"
        },
        {
            "some xlink definition 2"
        },
        {
            "sequence file definition"
        }
    ],
    "subunits": [
            "subunit definitions"
    ],
    "xlinkanalyzerVersion": "..."
}

Second, define the coordinates of the symmetry axis:

{
    "symmetry": {
        "sym_tr3ds": [

            {
                "name": "2fold",
                "axis": [0, 0, -1],
                "center": [246.39112398, 246.41114644, 248.600000],
                "type": "C2"

            }

        ]
    },
    "series": [
        "the series"
    ],
    "data": [
        {
            "some xlink definition 1"
        },
        {
            "some xlink definition 2"
        },
        {
            "sequence file definition"
        }
    ],
    "subunits": [
            "subunit definitions"
    ],
    "xlinkanalyzerVersion": "..."
}

Add specification of input PDB files

The input structures for the tutorial are in the in_pdbs/ directory:

Elp1.CTD.on5cqs.5cqr.model_ElNemo_mode7.pdb
Elp1_NTD_1st_propeller.pdb
Elp1_NTD_2nd_propeller.pdb
Elp2.pdb

Add them to the JSON like this:

{
    "symmetry": {
        "symmetry axis definition"
    },
    "series": [
        "the series"
    ],
    "data": [
        {
            "type": "pdb_files",
            "name": "pdb_files",
            "data": [
                        {
                            "foreach_serie": true,
                            "foreach_copy": true,
                            "components": [
                                { "name": "Elp1",
                                "subunit": "Elp1",
                                "domain": "propeller1",
                                "filename": "in_pdbs/Elp1_NTD_1st_propeller.pdb"
                                }
                            ]
                        },
                        {
                            "foreach_serie": true,
                            "foreach_copy": true,
                            "components": [
                                { "name": "Elp1",
                                "subunit": "Elp1",
                                "domain": "propeller2",
                                "filename": "in_pdbs/Elp1_NTD_2nd_propeller.pdb"
                                }
                            ]
                        },
                        {
                            "components": [
                                { "name": "Elp1",
                                "subunit": "Elp1",
                                "serie": "2fold",
                                "copies": [0],
                                "chain_id": "G",
                                "domain": "CTD",
                                "filename": "in_pdbs/Elp1.CTD.on5cqs.5cqr.model_ElNemo_mode7.pdb"},

                                { "name": "Elp1",
                                "subunit": "Elp1",
                                "serie": "2fold",
                                "copies": [1],
                                "chain_id": "H",
                                "domain": "CTD",
                                "filename": "in_pdbs/Elp1.CTD.on5cqs.5cqr.model_ElNemo_mode7.pdb"}
                            ]
                        },
                        {
                            "foreach_serie": true,
                            "foreach_copy": true,
                            "components": [
                                { "name": "Elp2",
                                "subunit": "Elp2",
                                "filename": "in_pdbs/Elp2.pdb"}
                            ]
                        },
                        {
                            "foreach_serie": true,
                            "foreach_copy": true,
                            "components": [
                                { "name": "Elp3",
                                "subunit": "Elp3",
                                "filename": "in_pdbs/Elp3.mono.pdb"}
                            ]
                        }

                ]

        },

        {
            "some xlink definition 1"
        },
        {
            "some xlink definition 2"
        },
        {
            "sequence file definition"
        }
    ],
    "subunits": [
            "subunit definitions"
    ],
    "xlinkanalyzerVersion": "..."
}

The foreach_serie and foreach_copy indicate the given PDB file specification will be applied to each serie with this subunit and for each copy within the series.

All PDB selections within the same components block will be grouped into a rigid body, unless a separate rigid_bodies block is specified and add_rbs_from_pdbs is set to False in Setting up the parameter file

Add pointers to fit libraries

{
    "symmetry": {
        "symmetry axis definition"
    },
    "series": [
        "the series"
    ],
    "data": [
        {
            "type": "pdb_files",
            "name": "pdb_files",
            "data": [
                        {
                            "foreach_serie": true,
                            "foreach_copy": true,
                            "components": [
                                { "name": "Elp1",
                                "subunit": "Elp1",
                                "domain": "propeller1",
                                "filename": "in_pdbs/Elp1_NTD_1st_propeller.pdb"
                                }
                            ],
                            "positions": "fits/search100000_metric_cam_inside0.6/emd_4151_binned.mrc/Elp1_NTD_1st_propeller.pdb/solutions_pvalues.csv",
                            "positions_type": "chimera",
                            "max_positions": 10000
                        },
                        {
                            "foreach_serie": true,
                            "foreach_copy": true,
                            "components": [
                                { "name": "Elp1",
                                "subunit": "Elp1",
                                "domain": "propeller2",
                                "filename": "in_pdbs/Elp1_NTD_2nd_propeller.pdb"
                                }
                            ],
                            "positions": "fits/search100000_metric_cam_inside0.6/emd_4151_binned.mrc/Elp1_NTD_2nd_propeller.pdb/solutions_pvalues.csv",
                            "positions_type": "chimera",
                            "max_positions": 10000
                        },
                        {
                            "components": [
                                { "name": "Elp1",
                                "subunit": "Elp1",
                                "serie": "2fold",
                                "copies": [0],
                                "chain_id": "G",
                                "domain": "CTD",
                                "filename": "in_pdbs/Elp1.CTD.on5cqs.5cqr.model_ElNemo_mode7.pdb"},

                                { "name": "Elp1",
                                "subunit": "Elp1",
                                "serie": "2fold",
                                "copies": [1],
                                "chain_id": "H",
                                "domain": "CTD",
                                "filename": "in_pdbs/Elp1.CTD.on5cqs.5cqr.model_ElNemo_mode7.pdb"}
                            ],
                            "positions": "fits/search100000_metric_cam_inside0.6/emd_4151_binned.mrc/Elp1.CTD.on5cqs.5cqr.model_ElNemo_mode7.pdb/solutions_pvalues.csv",
                            "positions_type": "chimera",
                            "max_positions": 1
                        },
                        {
                            "foreach_serie": true,
                            "foreach_copy": true,
                            "components": [
                                { "name": "Elp2",
                                "subunit": "Elp2",
                                "filename": "in_pdbs/Elp2.pdb"}
                            ],
                            "positions": "fits/search100000_metric_cam_inside0.6/emd_4151_binned.mrc/Elp2.pdb/solutions_pvalues.csv",
                            "positions_type": "chimera",
                            "max_positions": 10000
                        },
                        {
                            "foreach_serie": true,
                            "foreach_copy": true,
                            "components": [
                                { "name": "Elp3",
                                "subunit": "Elp3",
                                "filename": "in_pdbs/Elp3.mono.pdb"}
                            ],
                            "positions": "fits/search100000_metric_cam_inside0.6/emd_4151_binned.mrc/Elp3.mono.pdb/solutions_pvalues.csv",
                            "positions_type": "chimera",
                            "max_positions": 10000
                        }

                ]

        },

        {
            "some xlink definition 1"
        },
        {
            "some xlink definition 2"
        },
        {
            "sequence file definition"
        }
    ],
    "subunits": [
            "subunit definitions"
    ],
    "xlinkanalyzerVersion": "..."
}

And that’s it!