sokrypton
Question: Issue with automated model ranking in mmseqs notebook?
Yesterdays protein modeling gave the following log output with regard to the ranking of the five generated models:
`2023-09-22 18:52:35,633 alphafold2_ptm_model_1_seed_000 recycle=0 pLDDT=88.1 pTM=0.799 2023-09-22 18:54:13,264 alphafold2_ptm_model_1_seed_000 recycle=1 pLDDT=87.9 pTM=0.814 tol=0.512 2023-09-22 18:55:50,591 alphafold2_ptm_model_1_seed_000 recycle=2 pLDDT=88.6 pTM=0.824 tol=0.155 2023-09-22 18:57:27,719 alphafold2_ptm_model_1_seed_000 recycle=3 pLDDT=88.5 pTM=0.824 tol=0.218 2023-09-22 18:57:27,721 alphafold2_ptm_model_1_seed_000 took 416.7s (3 recycles) 2023-09-22 18:59:05,717 alphafold2_ptm_model_2_seed_000 recycle=0 pLDDT=89.2 pTM=0.827 2023-09-22 19:00:43,084 alphafold2_ptm_model_2_seed_000 recycle=1 pLDDT=89 pTM=0.839 tol=0.563 2023-09-22 19:02:20,305 alphafold2_ptm_model_2_seed_000 recycle=2 pLDDT=89.3 pTM=0.844 tol=0.184 2023-09-22 19:03:57,420 alphafold2_ptm_model_2_seed_000 recycle=3 pLDDT=88.9 pTM=0.836 tol=0.221 2023-09-22 19:03:57,422 alphafold2_ptm_model_2_seed_000 took 389.0s (3 recycles) 2023-09-22 19:05:35,861 alphafold2_ptm_model_3_seed_000 recycle=0 pLDDT=88.6 pTM=0.832 2023-09-22 19:07:13,289 alphafold2_ptm_model_3_seed_000 recycle=1 pLDDT=89.3 pTM=0.853 tol=0.514 2023-09-22 19:08:50,580 alphafold2_ptm_model_3_seed_000 recycle=2 pLDDT=89.4 pTM=0.853 tol=0.197 2023-09-22 19:10:27,531 alphafold2_ptm_model_3_seed_000 recycle=3 pLDDT=89 pTM=0.849 tol=0.124 2023-09-22 19:10:27,533 alphafold2_ptm_model_3_seed_000 took 389.0s (3 recycles) 2023-09-22 19:12:05,644 alphafold2_ptm_model_4_seed_000 recycle=0 pLDDT=88.9 pTM=0.831 2023-09-22 19:13:42,834 alphafold2_ptm_model_4_seed_000 recycle=1 pLDDT=89.1 pTM=0.841 tol=0.595 2023-09-22 19:15:19,840 alphafold2_ptm_model_4_seed_000 recycle=2 pLDDT=89.4 pTM=0.848 tol=0.162 2023-09-22 19:16:57,128 alphafold2_ptm_model_4_seed_000 recycle=3 pLDDT=88.9 pTM=0.842 tol=0.148 2023-09-22 19:16:57,131 alphafold2_ptm_model_4_seed_000 took 388.9s (3 recycles) 2023-09-22 19:18:35,480 alphafold2_ptm_model_5_seed_000 recycle=0 pLDDT=88.8 pTM=0.848 2023-09-22 19:20:12,740 alphafold2_ptm_model_5_seed_000 recycle=1 pLDDT=88.9 pTM=0.854 tol=0.752 2023-09-22 19:21:49,979 alphafold2_ptm_model_5_seed_000 recycle=2 pLDDT=89 pTM=0.852 tol=0.344 2023-09-22 19:23:27,137 alphafold2_ptm_model_5_seed_000 recycle=3 pLDDT=88.4 pTM=0.843 tol=0.172 2023-09-22 19:23:27,139 alphafold2_ptm_model_5_seed_000 took 388.8s (3 recycles)
2023-09-22 19:23:27,833 reranking models by 'plddt' metric 2023-09-22 19:23:27,834 rank_001_alphafold2_ptm_model_3_seed_000 pLDDT=89 pTM=0.849 2023-09-22 19:23:27,835 rank_002_alphafold2_ptm_model_4_seed_000 pLDDT=88.9 pTM=0.842 2023-09-22 19:23:27,835 rank_003_alphafold2_ptm_model_2_seed_000 pLDDT=88.9 pTM=0.836 2023-09-22 19:23:27,836 rank_004_alphafold2_ptm_model_1_seed_000 pLDDT=88.5 pTM=0.824 2023-09-22 19:23:27,837 rank_005_alphafold2_ptm_model_5_seed_000 pLDDT=88.4 pTM=0.843 2023-09-22 19:23:31,615 Done`
Not sure whether I have missed anything here with the data interpretation, but I assumed the automated ranking is based on maximum pLDDT value for which each recycle state is inspected individually for each generated model - and if pLDDT is equal, then the model with the lower pTM is chosen. If this is correct, shouldn't the ranking in the above log read as follows?
2023-09-22 19:15:19,840 alphafold2_ptm_model_4_seed_000 recycle=2 pLDDT=89.4 pTM=0.848 tol=0.162 2023-09-22 19:08:50,580 alphafold2_ptm_model_3_seed_000 recycle=2 pLDDT=89.4 pTM=0.853 tol=0.197 2023-09-22 19:02:20,305 alphafold2_ptm_model_2_seed_000 recycle=2 pLDDT=89.3 pTM=0.844 tol=0.184 2023-09-22 19:21:49,979 alphafold2_ptm_model_5_seed_000 recycle=2 pLDDT=89 pTM=0.852 tol=0.344 2023-09-22 18:55:50,591 alphafold2_ptm_model_1_seed_000 recycle=2 pLDDT=88.6 pTM=0.824 tol=0.155
Still testing... It appears to get stuck in endless minimization.
For default example, It works without issue.
On Thu, Sep 28, 2023, 2:34 AM MWNautilus @.***> wrote:
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