SecStrAnnotator:SecStrAPI

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Example of using SecStrAPI plugin in PyMOL:
> run https://webchem.ncbr.muni.cz/API/SecStr/Downloads/secstrapi_plugin.py
> annotate_sec_str 1tqn

The SecStrAPI allows programmatic access to precomputed secondary structure annotations. The annotations from SecStrAPI can also be easily visualized in PyMOL using SecStrAPI Plugin.


Requests


SecStrAPI format

The annotations are provided in SecStrAPI JSON format, demonstrated and explained below.

{
    "api_version": "1.0",                           
    "annotations": {
        "1tqn": {                                   # PDB ID
            "1tqnA": {                              # domain ID (unique domain identifier in SecStrAPI)
                "pdb": "1tqn",                      # PDB ID
                "chain_id": "A",                    # mmcif-style chain identifier (label_asym_id)
                "ranges": ":",                      # mmcif-style residue range (label_seq_id), : stands for the whole chain
                "auth_chain_id": "A",               # pdb-style chain identifier (auth_asym_id)
                "auth_ranges": ":",                 # pdb-style residue range (auth_seq_id), : stands for the whole chain
                "uniprot_id": "P08684",             # UniProt accession number
                "uniprot_name": "CP3A4_HUMAN",      # UniProt mnemonic identifier
                "domain_mappings": [                # list of mappings to source databases
                    {
                        "domain": "1tqnA00",        # domain ID in the source database, if available
                        "source": "CATH",           # name of source database
                        "family": "1.10.630.10",    # family ID in the source database
                        "pdb": "1tqn",              # PDB ID
                        "chain_id": "A",            # mmcif-style chain identifier (label_asym_id) of the domain in the source database
                        "ranges": "7:478"           # mmcif-style residue range (label_seq_id) of the domain in the source database (including the number before and after the colon)
                    },
                    {
                        "domain": null,
                        "source": "Pfam",
                        "family": "PF00067",
                        "pdb": "1tqn",
                        "chain_id": "A",
                        "ranges": "17:472"
                    }
                ],
                "secondary_structure_elements": [   # list of annotated secondary structure elements (SSEs)
                    {
                        "label": "1-1",             # SSE label
                        "chain_id": "A",            # mmcif-style chain identifier (label_asym_id)
                        "start": 50,                # mmcif-style residue number of the first residue (label_seq_id)
                        "end": 55,                  # mmcif-style residue number of the last residue (label_seq_id)
                        "auth_chain_id": "A",       # pdb-style chain identifier (auth_asym_id)
                        "auth_start": 71,           # pdb-style residue number of the first residue (auth_seq_id)
                        "auth_start_ins_code": "",  # residue insertion code of the first residue (pdbx_PDB_ins_code)
                        "auth_end": 76,             # pdb-style residue number of the last residue (auth_seq_id)
                        "auth_end_ins_code": "",    # residue insertion code of the last residue (pdbx_PDB_ins_code)
                        "type": "e",                # SSE type (h: helix, e: beta-strand)
                        "sheet_id": 1,              # beta-sheet identifier (all strands in the same sheet have the same sheet_id)
                        "color": "s164",            # pymol-style color assigned to this SSE (consistent through the whole family)
                        "metric_value": 2.5,        # measure of deviation from the template
                        "confidence": "high",       # confidence of the annotation (high: metric_value <= 10, medium: 10 < metric_value <= 20, low: metric_value > 20)
                        "sequence": "VWGFYD"        # amino acid sequence of the SSE
                    },
                    {
                        "label": "1-2",
                        "chain_id": "A",
                        "start": 58,
                        "end": 63,
                        "auth_chain_id": "A",
                        "auth_start": 79,
                        "auth_start_ins_code": "",
                        "auth_end": 84,
                        "auth_end_ins_code": "",
                        "type": "e",
                        "sheet_id": 1,
                        "color": "s186",
                        "metric_value": 2.03,
                        "confidence": "high",
                        "sequence": "QPVLAI"
                    },
                    {
                        "label": "B",
                        "chain_id": "A",
                        "start": 66,
                        "end": 76,
                        "auth_chain_id": "A",
                        "auth_start": 87,
                        "auth_start_ins_code": "",
                        "auth_end": 97,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s208",
                        "metric_value": 3.83,
                        "confidence": "high",
                        "sequence": "PDMIKTVLVKE"
                    }
                ],
                "beta_connectivity": [              # list of connections between strands in beta-sheets
                    [
                        "1-1",                      # label of the first strand
                        "1-2",                      # label of the second strand
                        -1                          # relative orientation of the strands (1: parallel, -1: antiparallel)
                    ]
                ],
                "rotation_matrix": [                # PyMOL object matrix used to align the domain to the template
                    0.0841438366722304,
                    -0.9907657680912565,
                    -0.10631560341088532,
                    -0.46321294579603234,
                    0.04653041207831938,
                    -0.10267083975128484,
                    0.99362649895048,
                    -0.12159261906614163,
                    -0.995366633709358,
                    -0.08855445467795255,
                    0.03746162109134595,
                    0.05273612685656731,
                    18.78404164503984,
                    23.992462979534775,
                    13.616655034021722,
                    1.0
                ],
                "comment": "Automatic annotation for 1tqn based on 2NNJ template. Program was called with these parameters: /home/adam/Workspace/C#/SecStrAnnot2_data/SecStrAPI/CytochromesP450-20200128/structures 2NNJ,A,: 1tqn,A,: --soft --label2auth --maxmetric 25,0.5,0.5 --verbose  Total value of used metric: 186.50"
            }
        }
    }
}



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