> 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/run-rocket-remotely-with-phenix.md).

# Run ROCKET Remotely with Phenix

You do **not** need in-house GPU access to try ROCKET.

[Phenix](https://www.phenix-online.org/) now hosts a preliminary remote launcher through `phenix.rocket`.

{% hint style="info" %}
This remote option is brand new. It is currently aimed at command-line use and is free for academics.
{% endhint %}

### What this does

`phenix.rocket` submits a ROCKET job to a remote Phenix server.

Use it when you want to run ROCKET without setting up local GPU hardware.

The command-line tool handles the job directory layout for you.

The method is inferred from the input files you provide.

### Current limitations

* Command-line only
* No GUI yet (we'll get there if there is demand!)
* No intermediate results during the run
* Current server capacity is limited to start as we gauge demand, just let us know if you end up waiting a long time.

{% hint style="warning" %}
The remote workflow in Phenix is brand new. If you hit issues, try `phenix.rocket` and reach out for help.
{% endhint %}

### Before you start

Prepare the same core inputs you would use for a normal ROCKET run.

One setting can be easy to miss:

* `file_id` must match the sequence identifier in your FASTA header

For example, if you use `file_id=1lj5`, the FASTA header should use `1lj5` as the sequence ID.

### X-ray example

Run:

```bash
phenix.rocket \
  1lj5-tng_withrfree.mtz \
  1lj5.fasta file_id=1lj5 \
  run_remotely=True
```

This submits the job to the remote server.

### Cryo-EM example

Run:

```bash
phenix.rocket \
  8p4pH.fasta \
  emd_17425_half_map_1.map \
  emd_17425_half_map_2.map \
  docked_model=8p4pH_docked.pdb \
  fixed_model=8p4pH-fixed-model-forchainH.pdb \
  resolution=7 \
  file_id=8p4pH \
  run_remotely=True
```

This uses the half maps plus optional fixed and docked models.

### Check job status

When a job is submitted, the output includes a `job_id`.

Use that ID to check whether the run is complete (example IDs shown below):

```bash
phenix.rocket job_id=1929cdd0-422b-4313-abe4-44095ebfc45d
phenix.rocket job_id=3b9447fa-67fa-41b9-84ef-43891cea2220
```

Use the same command again after completion to download the full job directory.

{% hint style="info" %}
`phenix.rocket` currently reports job completion status, but it does not stream intermediate refinement results.
{% endhint %}

### Practical notes

* You do not need to create the ROCKET directory structure yourself
* The tool decides whether the run is X-ray or cryo-EM from the inputs
* Not every ROCKET parameter is exposed yet in the remote launcher

### When to use this path

Use the Phenix route when:

* you want to try ROCKET quickly
* you do not have a local GPU available
* you want a Phenix-managed remote submission flow

Use the local ROCKET workflow when:

* you need full control over configs and parameters
* you want direct access to intermediate files
* you plan to iterate heavily on advanced settings

### Need help?

This feature is very new.

If something is unclear or does not behave as expected, please reach out so we can improve the workflow.

ROCKET Team <crew@rs-station.org>

Billy Poon (Phenix) <BKPoon@lbl.gov>