Questions about the new version of DMFold
Posted: Wed Feb 28, 2024 2:25 am
Hi, I was recently trying to predict protein complex using DMFold, and when I went to Step 2: Run_DeepMSA2.py, found that in the AF2 ranking step, there are some msa af2 predictions run templates_benchmark.py, such as aMSA, tthis should be the template search?
In fact, I later found that parameter
Is this normal?I0228 09:50:03.548033 46951213820416 templates_benchmark.py:883] Using precomputed obsolete pdbs /DeepMSA2/database/pdb_mmcif/obsolete.dat.
I0228 09:50:03.885781 46951213820416 tpu_client.py:54] Starting the local TPU driver.
I0228 09:50:03.886112 46951213820416 xla_bridge.py:212] Unable to initialize backend 'tpu_driver': Not found: Unable to find driver in registry given worker: local://
I0228 09:50:04.051980 46951213820416 xla_bridge.py:212] Unable to initialize backend 'tpu': Invalid argument: TpuPlatform is not available.
I0228 09:50:09.956907 46951213820416 run_alphafold_msa_benchmark.py:262] Have 5 models: ['model_1', 'model_2', 'model_3', 'model_4', 'model_5']
I0228 09:50:09.957167 46951213820416 run_alphafold_msa_benchmark.py:275] Using random seed 1822179567781964487 for the data pipeline
I0228 09:50:10.666351 46951213820416 hhsearch_benchmark.py:80] Launching subprocess "/DeepMSA2/anaconda3/envs/alphafold2nondocker/bin/hhsearch -i /tmp/tmpg1sihrja/query.a3m -o /tmp/tmpg1sihrja/output.hhr -maxseq 1000000 -z 100000 -Z 100000 -b 100000 -B 100000 -d /DeepMSA2/database/pdb70/pdb70"
I0228 09:50:10.773615 46951213820416 utils.py:36] Started HHsearch query
In fact, I later found that parameter
affects whether template retrieval is performed. I would like to ask, if I only evaluate the quality of msa, do I not need to perform template retrieval, then I can modify alphafold_seqcut=0.0?alphafold_seqcut