| # Tables and preview provenance |
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| Supporting-file paths below are relative to the repository’s `resources/` directory. Values in `archive_path` and `entry_directory` retain their documented repository-root and extraction-root meanings. |
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| ## Entry catalog |
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| `metadata/catalog/train.parquet` and `metadata/catalog/test.parquet` contain one row per EMD entry. `metadata/catalog/benchmark_targets.parquet` is the 618-row subset of the test catalog. |
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| | Field | Meaning | |
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| | `emd_id`, `pdb_id` | EMDB entry and the PDB identifier of the structure provided in the data archive | |
| | `split` | Fixed `train` or `test` membership | |
| | `benchmark_618` | Whether the entry belongs to the common 618-target benchmark | |
| | `resolution_angstrom` | Reported map resolution from `metadata/source_accessions.csv`, in Å | |
| | `title` | Deposited description from the source-accession table | |
| | `release_component` | Training download part or one of the two test archives | |
| | `archive_path`, `download_url` | Repository-relative path and direct URL of the complete containing archive | |
| | `entry_directory` | Entry directory inside the extracted training/test release | |
| | `has_aligned_cif` | Availability recorded by the released `metadata/Align_cif.json` list | |
| | `emdb_url`, `pdb_url`, `source_map_url` | Public accession pages and original map location | |
| | `map_release_date`, `structure_determination_method`, `sample_type` | Fields preserved from the source-accession table | |
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| Membership is checked against the fixed split lists. Training archive assignments come from the frozen release plan; test assignments are checked against both test-subset EMD lists. Catalog rows contain no server paths, credentials, or upload logs. |
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| ## Benchmark result table |
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| `benchmark/results.parquet` has one row per **EMD ID × method**: 618 targets and five methods, totaling 3,090 rows. It combines the five original CSVs under `benchmark/results/`. Original CSV values and bytes are preserved. |
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| - `method` identifies ModelAngelo, CryoAtom2, E3-CryoFold, EMProt or AF3. |
| - `emd_id`, `pdb_id`, `category`, `total_residues`, `resolution` and `n_chains` retain the released target descriptors. |
| - Metric names lose only their method prefix: for example, `ModelAngelo_gt_score` becomes `gt_score` in a row whose `method` is `ModelAngelo`. |
| - `tm_score`, `ca_rmsd`, residue coverage, sequence metrics and `gt_score` concern structure-to-reference agreement. |
| - `completeness` is the predicted-to-reference model-length ratio. It can exceed 1 and is not a bounded accuracy score. |
| - `cc_*`, `qscore`, `recall_qscore` and `map_score` describe the released map-agreement measurements. |
| - Ramachandran, rotamer, Cβ, clash, bond/angle, MolProbity and `geom_*` columns contain the released stereochemical measurements and composite components. |
| - `train_pident` and `train_bin` retain the identity annotations shipped in each method CSV. AF3 has no such columns in its source CSV, so the unified table leaves them null. Nulls are not zero measurements. |
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| No scores are recomputed or rescaled. Raw metrics use different units and directions; the table is a convenient view of the released evaluation outputs, not a new scoring protocol. When reproducing a published aggregate, use the paper's specified subset and aggregation rules. |
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| ## Archive index and checksums |
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| `metadata/catalog/archives.json` and `metadata/catalog/archives.parquet` list the same 71 files. `bytes` is the exact compressed size; `size_gb` uses decimal GB (10⁹ bytes). `sha256` hashes the complete compressed file. `entries` counts the map–model–sequence entries in a training/test archive; it is null for the mixed benchmark resource package. `metadata/checksums/SHA256SUMS` gives the same hashes with repository-relative paths. |
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| ## Density previews |
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| `benchmark/examples.parquet` contains an HF Image feature with embedded PNG bytes, plus example metadata and archive links. The ten maps are the existing examples in the benchmark resource package: nine benchmark-test entries and the training entry EMD-0719. |
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| Each image displays maximum-intensity projections along array axes 0, 1 and 2 of the stored MRC volume. Each projection is independently displayed between its 2nd and 99.5th percentiles, using a common color map. The axes refer to array storage order, not a standardized physical orientation. These display transformations do not alter the source maps and do not establish map–model alignment or quantify map quality. |
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| The overview figure counts entries in the fixed split lists and displays normalized histograms of reported resolutions from the source-accession table. All 17,809 resolutions are present. The plots and previews are derived browsing aids; the scientific archive files are unchanged. |
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| ## ModelAngelo training utility |
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| `benchmark/training_utility/MA_CryoAtlas.csv` and `MA_Cryo2StructData.csv` preserve the original Kaggle-released evaluation tables byte for byte. Each contains 618 target rows and one AVERAGE row. Both target sets equal the fixed 618-target benchmark. |
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| `benchmark/training_utility/results.parquet` contains only the 1,236 target rows. The `checkpoint` column identifies MA_CryoAtlas or MA_Cryo2StructData; the `cryo2struct_` prefix is removed from the latter condition's metric names to align columns. Values are neither recomputed nor rescaled. The original CSVs retain their original columns and aggregate rows. |
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| The corresponding predicted CIFs are in the resource archive's `training_utility/MA_CryoAtlas/` and `training_utility/MA_Cryo2StructData/` folders, 618 per condition. They were generated by the paper's retrained CNN checkpoints and are not serialized checkpoint weights. The official ModelAngelo reference remains part of the five-method benchmark. |
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