Recreate MSA Server Outputs Locally

Hi ColabFold team,

I'm trying to reproduce ColabFold server MSA results locally for multimer/complex searches, but I'm getting different outputs despite attempting to match the server configuration. I'd appreciate clarification on the exact workflow and parameters used by the server.
What I'm trying to achieve:
Reproduce the exact MSA search results from the ColabFold server locally for multimer protein complexes.
What I've tried:

• use the specific MMSeqs 18 release 8cc5ce3
• Referenced the config.json
• Tested various colabfold_search parameter combinations prefilter-mode use-env-pairing (pointing to the uniref db) both on CPU and GPU

Specific questions:

• For multimer searches with "pair_mode": "unpaired_paired", which exact script is used on the server? Is it the pairing script (second one in the backend)? What are the values for PAIRING_FILTER and PAIRING_FILTER_PROX parameters?

• What databases are actually used for pairing? Does the server use the same colabfold_envdb_202108_db for both regular environmental search and then uniref for the pairing?

• Are there any undocumented parameters or preprocessing steps that differ between the server and local colabfold_search? Could you provide the exact command-line equivalent that would reproduce the server's multimer search behavior?

Would greatly appreciate any guidance on matching the server's exact workflow locally. This would help ensure reproducibility for our large upcoming runs. @milot-mirdita @martin-steinegger
Thank you!

Start with MsaServer/config.json and the colabfold_search entry point, then compare the server's multimer pairing script, databases, and listed parameters. Done means documenting the exact workflow, preprocessing, parameter values, and command-line equivalent needed to reproduce the server outputs locally.