Multimer error on ColabFold 1.6.0

Hi,

After upgrading from ColabFold 1.5.5 to 1.6.0, I encountered a TypeError when running in multimer mode. The error does not occur in monomer mode.

Error logs:

2026-03-13 22:30:35,112 Running colabfold 1.6.0
2026-03-13 22:30:41,693 generated new fontManager
2026-03-13 22:30:42,041 Running on GPU
2026-03-13 22:30:42,180 Found 6 citations for tools or databases
2026-03-13 22:30:42,180 Query 2/1: BTB-domain_0 (length 59)
2026-03-13 22:30:42,383 Could not generate input features BTB-domain_0: Calling np.sum(generator) is deprecated.Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
Traceback (most recent call last):
  File "/usr/local/lib/python3.12/site-packages/colabfold/batch.py", line 1469, in run
    = generate_input_feature(query_seqs_unique, query_seqs_cardinality, unpaired_msa, paired_msa,
      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/colabfold/batch.py", line 931, in generate_input_feature
    input_feature = process_multimer_features(features_for_chain, min_num_seq=max_seq + 4)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/colabfold/batch.py", line 850, in process_multimer_features
    np_example = feature_processing.msa_pairing.merge_chain_features(
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/alphafold/data/msa_pairing.py", line 426, in merge_chain_features
    np_chains_list = _merge_homomers_dense_msa(np_chains_list)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/alphafold/data/msa_pairing.py", line 391, in _merge_homomers_dense_msa
    _merge_features_from_multiple_chains(chains, pair_msa_sequences=True)
  File "/usr/local/lib/python3.12/site-packages/alphafold/data/msa_pairing.py", line 363, in _merge_features_from_multiple_chains
    merged_example[feature_name] = np.sum(x for x in feats).astype(np.int32)
                                   ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/numpy/_core/fromnumeric.py", line 2419, in sum
    raise TypeError(
TypeError: Calling np.sum(generator) is deprecated.Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
2026-03-13 22:30:42,386 Done

Command used:

colabfold_batch --jobname-prefix BTB-domain --save-all  --random-seed 654321 --model-type=alphafold2_multimer_v3 --amber --use-gpu-relax sp_Q9Y2Y4_ZBT32_HUMAN_29-87_Homodimer_Zinc_finger_and_BTB_domain-containing_protein_32_OS_Homo_sapiens_OX_9606_GN_ZBTB32_PE_1_SV_1.a3m predictions

Do you have any ideas on how to solve this problem?

Start with the multimer traceback in colabfold/batch.py, then inspect alphafold/data/msa_pairing.py at _merge_features_from_multiple_chains. Reproduce the failure with the provided colabfold_batch command in multimer mode and compare it with monomer mode. Done means the multimer run no longer raises the NumPy TypeError.