Not enough transformations between subunits, there should be one connected component!

[spark159]

Hi, I am trying to assemble the protein complex but the ran was failed.

I just ran two subunit complex for test, so I guess there should be no issue of connectivity since this is just a dimer.

However, the assembly process was failed and output log said that there are not enough transformations between subunits.

I made predicted PDB files from AlphaFold3 servers

Could you help me to figure out what is problem in this run?

I am attaching the input json (for AF3 and CombFold) and CombFold log file here. ATPmodule_example_subunits_AF3_pairs.json ATPmodule_example_subunits_CF.json output.log

And here are output during the run

--- Searching for subunits in supplied PDB files found full ACTB:0-375 in ACTB:0-375_ACTL6A:0-429_model_4.pdb chain A found full ACTL6A:0-429 in ACTB:0-375_ACTL6A:0-429_model_4.pdb chain B found full ACTB:0-375 in ACTB:0-375_ACTL6A:0-429_model_3.pdb chain A found full ACTL6A:0-429 in ACTB:0-375_ACTL6A:0-429_model_3.pdb chain B found full ACTB:0-375 in ACTB:0-375_ACTL6A:0-429_model_2.pdb chain A found full ACTL6A:0-429 in ACTB:0-375_ACTL6A:0-429_model_2.pdb chain B found full ACTB:0-375 in ACTB:0-375_ACTL6A:0-429_model_0.pdb chain A found full ACTL6A:0-429 in ACTB:0-375_ACTL6A:0-429_model_0.pdb chain B found full ACTB:0-375 in ACTB:0-375_ACTL6A:0-429_model_1.pdb chain A found full ACTL6A:0-429 in ACTB:0-375_ACTL6A:0-429_model_1.pdb chain B --- Extracting representative subunits (for each subunit, its best scored model in the PDBs folder) rep ACTB:0-375 has plddt score 92.39168 rep ACTL6A:0-429 has plddt score 90.79522144522144 --- Extracting pairwise transformations between subunits (from each PDB file with 2 or more subunits)

• Extracting pairwise transformations from file /Users/sangwoopark/Projects/CombFold/data/test/ACTB:0-375_ACTL6A:0-429_model_4.pdb /Users/sangwoopark/Projects/CombFold/CombinatorialAssembler/AF2trans.out /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/ACTB:0-375_1_375.pdb /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/ACTL6A:0-429_1_429.pdb /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/sample1_ACTB:0-375.pdb /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/sample2_ACTL6A:0-429.pdb
• Extracting pairwise transformations from file /Users/sangwoopark/Projects/CombFold/data/test/ACTB:0-375_ACTL6A:0-429_model_3.pdb /Users/sangwoopark/Projects/CombFold/CombinatorialAssembler/AF2trans.out /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/ACTB:0-375_1_375.pdb /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/ACTL6A:0-429_1_429.pdb /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/sample1_ACTB:0-375.pdb /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/sample2_ACTL6A:0-429.pdb
• Extracting pairwise transformations from file /Users/sangwoopark/Projects/CombFold/data/test/ACTB:0-375_ACTL6A:0-429_model_2.pdb /Users/sangwoopark/Projects/CombFold/CombinatorialAssembler/AF2trans.out /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/ACTB:0-375_1_375.pdb /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/ACTL6A:0-429_1_429.pdb /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/sample1_ACTB:0-375.pdb /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/sample2_ACTL6A:0-429.pdb
• Extracting pairwise transformations from file /Users/sangwoopark/Projects/CombFold/data/test/ACTB:0-375_ACTL6A:0-429_model_0.pdb /Users/sangwoopark/Projects/CombFold/CombinatorialAssembler/AF2trans.out /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/ACTB:0-375_1_375.pdb /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/ACTL6A:0-429_1_429.pdb /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/sample1_ACTB:0-375.pdb /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/sample2_ACTL6A:0-429.pdb
• Extracting pairwise transformations from file /Users/sangwoopark/Projects/CombFold/data/test/ACTB:0-375_ACTL6A:0-429_model_1.pdb /Users/sangwoopark/Projects/CombFold/CombinatorialAssembler/AF2trans.out /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/ACTB:0-375_1_375.pdb /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/ACTL6A:0-429_1_429.pdb /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/sample1_ACTB:0-375.pdb /Users/sangwoopark/Projects/CombFold/ATPmodule_example/_unified_representation/transformations/temp_transformations/sample2_ACTL6A:0-429.pdb found 5 transformations between ACTB:0-375 and ACTL6A:0-429 --- Finished building unified representation --- Running combinatorial assembly algorithm, may take a while --- Finished combinatorial assembly, writing output models Could not assemble, exiting

Thanks in advance!!

[spark159]

I think I found the problem. I have ":" in the chain name which was recognized by program as delimiter.

You can close the issue. Thanks!