Request on how to generate extra MSA files available from public server vs locally using `colabfold_search`

Hello ColabFold team!,

First, thank you so much for maintaining, updating and creating ColabFold! I really appreciate your team's efforts!

I noticed that runningcolabfold_batch using the public server as MSA source , I see that the output has 3 types of MSA files namely ( as shown below copied from Ref. #580 ) -- heterodimer_2.a3m , pair.a3m and uniref.a3m files.

However, when I use colabfold_search on my locally created database (database was created about ~6 months ago) I only get the MSA file heterodimer_2.a3m. Passing heterodimer_2.a3m file to colabfold_batch doesn't generate any additional MSA files as above.

So my question is --

• are there scripts/ways to get the pair.a3m and uniref.a3m files using colabfold_search on my locally created database?
• It will be also great if you can elaborate on what are the contents of pair.a3m and uniref.a3m files and how they affect the structure prediction accuracy.

Results from using colabfold_batch where the MSAs come from public server

.
├── cite.bibtex
├── config.json
├── log.txt
├── heterodimer_2.a3m
├── heterodimer_2_coverage.png
├── heterodimer_2.done.txt
├── heterodimer_2_env
│   ├── bfd.mgnify30.metaeuk30.smag30.a3m
│   ├── msa.sh
│   ├── out.tar.gz
│   ├── pdb70.m8
│   ├── templates_101
│   │   ├── 7x8v.cif
│   │   ├── pdb70_a3m.ffdata
│   │   ├── pdb70_a3m.ffindex
│   │   ├── pdb70_cs219.ffdata
│   │   └── pdb70_cs219.ffindex -> pdb70_a3m.ffindex
│   ├── templates_102
│   │   ├── 1t1h.cif
│   │   ├── 2c2l.cif
│   │   ├── 2c2v.cif
│   │   ├── 2f42.cif
│   │   ├── 2oxq.cif
│   │   ├── 5olm.cif
│   │   ├── 6fga.cif
│   │   ├── 6s53.cif
│   │   ├── 7bbd.cif
│   │   ├── 7c96.cif
│   │   ├── 8a58.cif
│   │   ├── pdb70_a3m.ffdata
│   │   ├── pdb70_a3m.ffindex
│   │   ├── pdb70_cs219.ffdata
│   │   └── pdb70_cs219.ffindex -> pdb70_a3m.ffindex
│   └── uniref.a3m
├── heterodimer_2_pae.png
├── heterodimer_2_pairgreedy
│   ├── out.tar.gz
│   ├── pair.a3m
│   └── pair.sh
├── heterodimer_2_plddt.png
├── heterodimer_2_predicted_aligned_error_v1.json
├── heterodimer_2_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
├── heterodimer_2_relaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb
├── heterodimer_2_relaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb
├── heterodimer_2_relaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb
├── heterodimer_2_relaxed_rank_005_alphafold2_multimer_v3_model_4_seed_000.pdb
├── heterodimer_2_scores_rank_001_alphafold2_multimer_v3_model_1_seed_000.json
├── heterodimer_2_scores_rank_002_alphafold2_multimer_v3_model_3_seed_000.json
├── heterodimer_2_scores_rank_003_alphafold2_multimer_v3_model_5_seed_000.json
├── heterodimer_2_scores_rank_004_alphafold2_multimer_v3_model_2_seed_000.json
├── heterodimer_2_scores_rank_005_alphafold2_multimer_v3_model_4_seed_000.json
├── heterodimer_2_template_domain_names.json
├── heterodimer_2_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
├── heterodimer_2_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb
├── heterodimer_2_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb
├── heterodimer_2_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb
└── heterodimer_2_unrelaxed_rank_005_alphafold2_multimer_v3_model_4_seed_000.pdb

Results from locally created MSA file heterodimer_2.a3m using colabfold_search from local database followed by passing to colabfold_batch

.
├── cite.bibtex
├── config.json
├── log.txt
├── heterodimer_2.a3m
├── heterodimer_2_coverage.png
├── heterodimer_2.done.txt
├── heterodimer_2_pae.png
├── heterodimer_2_plddt.png
├── heterodimer_2_predicted_aligned_error_v1.json
├── heterodimer_2_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
├── heterodimer_2_relaxed_rank_002_alphafold2_multimer_v3_model_5_seed_000.pdb
├── heterodimer_2_relaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb
├── heterodimer_2_relaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb
├── heterodimer_2_relaxed_rank_005_alphafold2_multimer_v3_model_4_seed_000.pdb
├── heterodimer_2_scores_rank_001_alphafold2_multimer_v3_model_1_seed_000.json
├── heterodimer_2_scores_rank_002_alphafold2_multimer_v3_model_5_seed_000.json
├── heterodimer_2_scores_rank_003_alphafold2_multimer_v3_model_3_seed_000.json
├── heterodimer_2_scores_rank_004_alphafold2_multimer_v3_model_2_seed_000.json
├── heterodimer_2_scores_rank_005_alphafold2_multimer_v3_model_4_seed_000.json
├── heterodimer_2_template_domain_names.json
├── heterodimer_2_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
├── heterodimer_2_unrelaxed_rank_002_alphafold2_multimer_v3_model_5_seed_000.pdb
├── heterodimer_2_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb
├── heterodimer_2_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb
├── heterodimer_2_unrelaxed_rank_005_alphafold2_multimer_v3_model_4_seed_000.pdb
└── templates
    ├── 1t1h.cif
    ├── 2c2l.cif
    ├── 2c2v.cif
    ├── 2f42.cif
    ├── 2oxq.cif
    ├── 5olm.cif
    ├── 6fga.cif
    ├── 6s53.cif
    ├── 7bbd.cif
    ├── 7c96.cif
    ├── 7x8v.cif
    ├── pdb70_a3m.ffdata
    ├── pdb70_a3m.ffindex
    ├── pdb70_cs219.ffdata
    └── pdb70_cs219.ffindex

Start by tracing the colabfold_search and colabfold_batch entry points and comparing the listed public-server and local output trees. Check how heterodimer_2.a3m, pair.a3m, and uniref.a3m are produced; done means documenting whether local generation supports both files and explaining their roles.