> For the complete documentation index, see [llms.txt](https://rocket-9.gitbook.io/rocket-docs/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://rocket-9.gitbook.io/rocket-docs/api/rk.preprocess.md). # rk.preprocess `rk.preprocess` performs the preprocessing of predicted protein structures for **ROCKET**. It runs **OpenFold inference**, processes structures using **Phenix**, and performs **Molecular Replacement or Cryo-EM Docking**. ### TL;DR. 1. A typical preprocessing command for **X-ray** datasets (for our human serpin case) ```bash rk.preprocess \ --file_id 1lj5 \ --method xray \ --output_dir ./1lj5_processed \ --max_recycling_iters 20 \ --use_deepspeed_evoformer_attention ``` It requires working in the path with preexisting data files organized as: ``` . ├── 1lj5_data │ └── 1lj5-tng_withrfree.mtz ├── 1lj5_fasta │ └── 1lj5.fasta ├── alignments │ └── 1lj5 │ ├── bfd_uniclust_hits.a3m │ ├── mgnify_hits.a3m │ ├── pdb70_hits.hhr │ └── uniref90_hits.a3m ``` **Note**: If the MTZ file provided contains more than one set of relevant columns (e.g. intensities and errors + structure factor amplitudes and errors), Phaser will pick the best set for you – it's likely better to work from the intensities if available! If you absolutely want to use a specific set of columns, you can provide an MTZ that contains only that data. 2. A typical preprocessing command for **Cryo-EM** map datasets (for our groEL case): ```bash rk.preprocess \ --file_id 8p4pA \ --resolution 9.6 \ --method cryoem \ --output_dir 8p4pA_processed \ --predocked_model 8p4pA_data/8p4pA_docked.pdb \ --fixed_model 8p4pA_data/8p4pA-fixed-model-forchainA.pdb \ --map1 8p4pA_data/emd_17425_half_map_1.map \ --map2 8p4pA_data/emd_17425_half_map_2.map \ --max_recycling_iters 20 \ --use_deepspeed_evoformer_attention ``` If you already have a `--predocked_model` and only a single post-processed map, you can use `--map` alone: ```bash rk.preprocess \ --file_id 8p4pA \ --resolution 9.6 \ --method cryoem \ --output_dir 8p4pA_processed \ --predocked_model 8p4pA_data/8p4pA_docked.pdb \ --fixed_model 8p4pA_data/8p4pA-fixed-model-forchainA.pdb \ --map 8p4pA_data/emd_17425_postprocessed.map \ --max_recycling_iters 20 \ --use_deepspeed_evoformer_attention ``` **Note:** `--map` alone only works when ROCKET can skip docking because you already supplied a predocked model. If ROCKET still needs to perform a docking search, you must provide both half maps with `--map1` and `--map2`. It requires preexisting data files organized as: ``` . ├── 8p4pA_fasta │ └── 8p4pA.fasta ├── alignments │ └── 8p4pA │ ├── bfd_uniclust_hits.a3m │ ├── pdb70_hits.hhr │ └── uniref90_hits.a3m ├── 8p4pA_data │ ├── emd_17425_half_map_1.map │ ├── emd_17425_half_map_2.map │ ├── emd_17425_postprocessed.map │ ├── 8p4pA-fixed-model-forchainA.pdb │ └── 8p4pA_docked.pdb ``` ### Input Parameters | Argument | Description | | ------------------------------------- | ---------------------------------------------------------------------------------------------------------------------- | | `--file_id` | Identifier for input files. | | `--resolution` | The best resolution for cryoEM map. Not used for x-ray case. | | `--method` | Choose `"xray"` (calls Phaser) or `"cryoem"` (calls EMPlacement). | | `--output_dir` | Directory to store results (default: `"preprocessing_output"`). | | `--precomputed_alignment_dir` | Path to OpenFold precomputed alignments (default: `"alignments/"`). | | `--max_recycling_iters` | N\_recyclings for initial predictions (default: 4) | | `--use_deepspeed_evoformer_attention` | Flag, whether to use the DeepSpeed evoformer attention layer. Must have deepspeed installed in the environment | | `--jax_params_path` | Path to JAX parameter file (`"params_model_1_ptm.npz"`). Default `None`, will use system env var `$OPENFOLD_RESOURCES` | The scripts expects input files organized as follows: ``` / ├── {file_id}_fasta/ │ └── {file_id}.fasta # FASTA file containing the chain to refine │ # Header should be "> {file_id}" │ ├── {file_id}_data/ │ ├── *.mtz # For X-ray data │ ├── *_half_map*.mrc # For Cryo-EM data │ └── # e.g., predicted or docked models │ ├── alignments/ # (default: --precomputed_alignment_dir) │ └── {file_id} | └──*.a3m / *.hhr ``` #### Additional Parameters for Cryo-EM (`--method cryoem`) | Argument | Description | | -------------------- | -------------------------------------------------------------------------------------------------------------------------- | | `--map` | Path to a single post-processed map. Use this only when `--predocked_model` is provided and docking can be skipped. | | `--map1` | Path to **Half-map 1**. Required when ROCKET needs to run a docking search. | | `--map2` | Path to **Half-map 2**. Required when ROCKET needs to run a docking search. | | `--full_composition` | FASTA file containing sequences of everything expected to be in the reconstruction, whether there is a model for it or not | | | | #### Optional Arguments | Argument | Description | | ------------------- | ---------------------------------------------------- | | `--predocked_model` | Path to an already docked model (default: `None`). | | `--fixed_model` | Optional fixed model contribution (default: `None`). | **Note:** When `--predocked_model` is present, `--map` is enough if you only have one post-processed map. Without a predocked model, or whenever docking still needs to be searched, use `--map1` and `--map2`. ## Outputs After execution, results will be structured in the `--output_dir` directory: ``` output_dir/ |── {file_id}.fasta # FASTA file containing the chain to refine, copied from input ├── alignments/ # MSA files for the input sequence, copied from input | └──*.a3m / *.hhr │── predictions/ # OpenFold structure predictions and pkl files │ └── xxx_processed_feats.pickle # Processed feature dict with cluster profiles │── ROCKET_inputs/ # Final outputs for ROCKET main trunk │ ├── {file_id}-pred-aligned.pdb # Aligned prediction with pseudo-Bs │ ├── {file_id}-Edata.mtz # Experimental data in LLG convention ├── ROCKET_config_phase1.yaml # Automatically generated config file for rk.refine phase1 run ├── ROCKET_config_phase2.yaml. # Automatically generated config file for rk.refine phase2 run │── processed_predicted_files/ # Processed predictions from Phenix (including trimmed confidence loops) │── docking_outputs/ # Cryo-EM docking results (if exists) │── phaser_files/ # X-ray molecular replacement results (if exists) ``` --- # Agent Instructions This documentation is published with GitBook. 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