From 532a008f0ca135c4b6553b9eff446425e55daf9c Mon Sep 17 00:00:00 2001 From: Sean Wang Date: Wed, 20 May 2026 16:40:49 -0700 Subject: [PATCH 1/2] Preserve user-supplied templates in batched MMseqs2-GPU path --- src/alphafold3/data/pipeline.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/alphafold3/data/pipeline.py b/src/alphafold3/data/pipeline.py index 9b32362..42cdeba 100644 --- a/src/alphafold3/data/pipeline.py +++ b/src/alphafold3/data/pipeline.py @@ -1709,12 +1709,17 @@ def process_batch( for hit, struc in template_hits.get_hits_with_structures() ] + # Preserve any user-supplied templates from the input JSON. + # When the user provided templates, run_template_search was False + # above, so pdb_templates is []; we still want their templates kept. + user_templates = list(chain.templates) if chain.templates else [] + # Get Foldseek templates and merge foldseek_tmpls = self._get_foldseek_templates( chain.sequence ) templates = self._merge_templates( - pdb_templates, foldseek_tmpls + user_templates + pdb_templates, foldseek_tmpls ) processed_chain = folding_input.ProteinChain( From 34d788ae1888b0d36c97b871302bdf1a4d6a1b3b Mon Sep 17 00:00:00 2001 From: Sean Wang Date: Wed, 20 May 2026 16:45:29 -0700 Subject: [PATCH 2/2] Preserve user-supplied templates in batched MMseqs2-GPU path --- src/alphafold3/data/pipeline.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/alphafold3/data/pipeline.py b/src/alphafold3/data/pipeline.py index 42cdeba..cd8bf50 100644 --- a/src/alphafold3/data/pipeline.py +++ b/src/alphafold3/data/pipeline.py @@ -1710,8 +1710,6 @@ def process_batch( ] # Preserve any user-supplied templates from the input JSON. - # When the user provided templates, run_template_search was False - # above, so pdb_templates is []; we still want their templates kept. user_templates = list(chain.templates) if chain.templates else [] # Get Foldseek templates and merge