# Installing ROCKET ### 1. Install OpenFold We forked OpenFold and cleaned up a few installation details for ROCKET users. {% hint style="info" %} Plan for a GPU machine, enough free disk space, and a clean environment before you start. {% endhint %} **Note**: The ⁠openfold installation requires approximately 6 GB of free space to download weights. Please ensure you start in a directory with sufficient available space. **Note**: To ensure a smooth installation and execution of ROCKET, install on a GPU machine that matches the hardware you’ll use in production. In other words, for HPC users, if you plan to run your code on a node with a particular GPU model, request the same GPU model when you install OpenFold. This is important because the installation process performs hardware-specific compilation. We also recommend using GPUs with CUDA Compute Capability 8.0 or higher. 1. Clone our fork of the OpenFold repo, switch to the `pl_upgrades` branch to work with CUDA 12: ```bash git clone https://github.com/minhuanli/rocket_openfold.git cd rocket_openfold git checkout pl_upgrades ``` 2. Create a conda or mamba environment with `environment.yml`. Mamba is recommended because the dependency set is large. If you use Conda instead, replace `mamba` with `conda` in the commands below. **Note**: If you work with an HPC cluster with package management like `module`, purge all your modules before this step to avoid conflicts. ```bash mamba env create -n -f environment.yml mamba activate ``` We keep `flash-attn` outside the YAML so you can install a compatible version manually. This OpenFold branch uses PyTorch 2.1. The latest `flash-attn` will not work. The `--no-build-isolation` flag also lets `ninja` speed up compilation. 3. Install a compatible `flash-attn` build: ```bash pip install flash-attn==2.2.2 --no-build-isolation ``` 4. Run the setup script: ```bash ./scripts/install_third_party_dependencies.sh ``` Add the following lines to `/etc/conda/activate.d/env_vars.sh`. Create the file if it does not exist. ```bash #!/bin/sh export LIBRARY_PATH=$CONDA_PREFIX/lib:$LIBRARY_PATH export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH ``` This makes the library path update happen automatically whenever the environment is activated. 5. Download AlphaFold2 weights and set the resource path: ```bash ./scripts/download_alphafold_params.sh ./openfold/resources ``` **Note:** You can also download OpenFold weights if you want to test them. Append the following line to the same `env_vars.sh` file: ```bash export OPENFOLD_RESOURCES="/openfold/resources" ``` `` should be the output of `pwd -P` you get from the OpenFold repo path. Deactivate and reactivate your environment. Then confirm the path: ```bash echo $OPENFOLD_RESOURCES ``` 6. Check your OpenFold build with unit tests: ```bash ./scripts/run_unit_tests.sh ``` Ensure you see no errors: ``` ... Time to load evoformer_attn op: 243.8257336616516 seconds ............s...s.sss.ss.....sssssssss.sss....ssssss..s.s.s.ss.s......s.s..ss...ss.s.s....s........ ---------------------------------------------------------------------- Ran 117 tests in 275.889s OK (skipped=41) ``` ### 2. Install Phenix Required for automatic preprocessing and post-refinement. {% hint style="warning" %} Use an absolute install path for Phenix. It avoids path issues later. {% endhint %} [Phenix](https://phenix-online.org/) is required for automatic data preprocessing and for post-refinement when polishing final model geometry. Follow the steps below to install it and **add the path to the system environment variables**: 1. Download the latest Python 3 nightly build from . Use at least version `2.0-5936`. 2. Run the installer ```bash bash phenix-installer-2.0rc1-5936-.sh ``` You will be prompted to type your preferred path of installation, after specifying it, you will see: ``` Phenix will now be installed into this location: /phenix-2.0-5936 ``` **Note**: `` must be an absolute path. The installer will create `/phenix-2.0-5936` and install there. 3. Append the following line to the same `env_vars.sh` file: ```bash export PHENIX_ROOT="/phenix-2.0-5936" ``` `` is the path you chose in the previous step. Deactivate and reactivate your environment. Then confirm the path: ```bash echo $PHENIX_ROOT ``` ### 3. Install ROCKET Move to a separate parent directory, clone ROCKET, then install it with `pip`: ```bash git clone https://github.com/alisiafadini/ROCKET.git cd ROCKET pip install . ``` This also installs dependencies such as `SFcalculator` and `reciprocalspaceship`. **Note:** If you get errors about incompatibility of `prompt_toolkit`, ignore them. For editable install mode, run: ```bash pip install -e . ``` Run `rk.score --help` after installation. If it prints normal help text without errors, the install is ready. {% hint style="success" %} Once this works, move on to the X-ray or cryo-EM setup tutorial. {% endhint %} [Create an issue](https://github.com/alisiafadini/ROCKET/issues) in our repo --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://rocket-9.gitbook.io/rocket-docs/getting-started/installing-rocket.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. 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