Run ROCKET Remotely with Phenix

Launch ROCKET on the Phenix server when you do not have local GPU access

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

Phenix now hosts a preliminary remote launcher through phenix.rocket.

This remote option is brand new. It is currently aimed at command-line use and is free for academics.

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.

The remote workflow in Phenix is brand new. If you hit issues, try phenix.rocket and reach out for help.

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:

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:

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:

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.

phenix.rocket currently reports job completion status, but it does not stream intermediate refinement results.

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 [e-mail]

Billy Poon (Phenix) [e-mail]