YoshitakaMo / localcolabfold

ColabFold on your local PC
MIT License
613 stars 135 forks source link

Why does pLDDT get lower with the increase of recycle? Shouldn't the confidence level get higher with recycle #242

Open 15019669985 opened 4 months ago

15019669985 commented 4 months ago

2024-06-22 02:36:48,732 Query 1/2411: D DRAMP21215 (length 4) coMPLETE: 100%|/11//111/1/11l 150/15o [elapsed: o0:02 remaini 2024-06-22 02:37:04,806 Padding length to 14 2024-06-22 02:42:02,380 alphafold2_ptm_model_1_seed_000 recycle=0 pLDDT=66.9 pTM=0.0864 2024-06-22 02:46:21,907 alphafold2_ptm_model_1_seed_000 recycle=1 pLDDT=28.6 pTM=0.00161 tol=3.87 2024-06-22 02:50:44,827 alphafold2_ptm_model_1_seed_000 recycle=2 pLDDT=36 pTM=0.00242 tol=17 2024-06-22 02:55:10,542 alphafold2_ptm_model_1_seed_000 recycle=3 pLDDT=16 pTM=0.000763 tol=16.2 2024-06-22 02:55:10,544 alphafold2_ptm_model_1_seed_000 took 1085.7s (3 recycles) 2024-06-22 02:55:10,773 reranking models by 'plddt' metric 2024-06-22 02:55:14,200 Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. 2024-06-22 02:55:41,239 Relaxation took 30.5s 2024-06-22 02:55:41,240 rank_001_alphafold2_ptm_model_1_seed_000 pLDDT=16 pTM=0.000763 2024-06-22 02:55:41,914 Query 2/2411: DRAMP04172 (length 5) COMPLETE: 1OO%I 150/150 [elapsed: 00:01 remaini

Is it because my sequence is too short, or is it because I just used the cpu