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Something seems to be wrong in input.md #232

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Maikuraky opened this issue Dec 24, 2024 · 1 comment
Closed

Something seems to be wrong in input.md #232

Maikuraky opened this issue Dec 24, 2024 · 1 comment
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bug Something isn't working documentation Improvements or additions to documentation question Further information is requested

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@Maikuraky
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Maikuraky commented Dec 24, 2024

{
  "name": "Hello fold",
  "modelSeeds": [10, 42],
  "sequences": [
    {
      "protein": {
        "id": "A",
        "sequence": "PVLSCGEWQL",
        "modifications": [
          {"ptmType": "HY3", "ptmPosition": 1},
          {"ptmType": "P1L", "ptmPosition": 5}
        ],
        "unpairedMsa": ...,
      }
    },
    {
      "protein": {
        "id": "B",
        "sequence": "RPACQLW",
        "templates": [
          {
            "mmcif": ...,
            "queryIndices": [0, 1, 2, 4, 5, 6],
            "templateIndices": [0, 1, 2, 3, 4, 8]
          }
        ]
      }
    },
    {
      "dna": {
        "id": "C",
        "sequence": "GACCTCT",
        "modifications": [
          {"modificationType": "6OG", "basePosition": 1},
          {"modificationType": "6MA", "basePosition": 2}
        ]
      }
    },
    {
      "rna": {
        "id": "E",
        "sequence": "AGCU",
        "modifications": [
          {"modificationType": "2MG", "basePosition": 1},
          {"modificationType": "5MC", "basePosition": 4}
        ],
        "unpairedMsa": ...
      }
    },
    {
      "ligand": {
        "id": ["F", "G", "H"],
        "ccdCodes": ["ATP"]
      }
    },
    {
      "ligand": {
        "id": "I",
        "ccdCodes": ["NAG", "FUC"]
      }
    },
    {
      "ligand": {
        "id": "Z",
        "smiles": "CC(=O)OC1C[NH+]2CCC1CC2"
      }
    }
  ],
  "bondedAtomPairs": [
    [["A", 1, "CA"], ["B", 1, "CA"]],
    [["A", 1, "CA"], ["G", 1, "CHA"]],
    [["J", 1, "O6"], ["J", 2, "C1"]]
  ],
  "userCCD": ...,
  "dialect": "alphafold3",
  "version": 2
}

There seems to be no Entity J in the current example input json, and Entity I has two strings in ccdCodes but only one id.

RNA Multiple Sequence Alignment
RNA unpairedMsa can be either:

1. Unset (or set explicitly to null). AlphaFold 3 won't build MSA for this RNA chain.
2. Set to an empty string (""). AlphaFold 3 won't build MSA and will run MSA-free for this RNA chain.
3. Set to a non-empty A3M string. AlphaFold 3 will use the provided MSA for this RNA chain.

There “Unset (or set explicitly to null). AlphaFold 3 won't build MSA for this RNA chain.” may be “Unset (or set explicitly to null). AlphaFold 3 will build MSA for this RNA chain.”?

@Augustin-Zidek Augustin-Zidek added bug Something isn't working documentation Improvements or additions to documentation question Further information is requested labels Dec 24, 2024
@Augustin-Zidek
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Hi, thanks for reporting this. The bonded atom pair for entity J is incorrect -- this is a typo and it should be entity I and I have fixed it in a647a31.

Entity I is a two-residue ligand, that is why it has only one ID and the bond between the two residues explicitly specified in bondedAtomPairs.

For the MSA question:

If I don't specify the RNA:

"rna": {
  "id": "E",
  "sequence": "AGCU",
}

or I specify the unpairedMsa as null:

"rna": {
  "id": "E",
  "sequence": "AGCU",
  "unpairedMsa": null
}

AlphaFold 3 will search for this RNA's MSA.

However, if I specify the RNA as an empty string:

"rna": {
  "id": "E",
  "sequence": "AGCU",
  "unpairedMsa": ""
}

AlphaFold 3 will treat this as MSA-free RNA and won't search for MSA of this sequence.

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