Comments (3)
Gordon5-AI
commented on August 19, 2024
Same questions, this work has been done very well, but the specific meaning of some parameters is not detailed enough. It will be more helpful if you can provide a detailed tutorial later.
Thanks!
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donglg1309
commented on August 19, 2024
The PSSM flags are confusing based on the current version. A further PSSM help script will be helpful. It seems that the file '/home/swang523/RLcage/capsid/monomersfordesign/8-16-21/pssm_rainity_final_8-16-21_int/build_0.2089_0.98_0.4653_19_2.00_0.005745.pssm' cannot be accessed.
Thanks!
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dauparas
commented on August 19, 2024
Sorry, I forgot to paste this example here: https://github.com/dauparas/ProteinMPNN/blob/main/examples/submit_example_pssm.sh I hope this helps!
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Related Issues (20)
- Questions about model weights
- .Fa Output reorganization question
- Sampling temperature for flexible chains
- what pdbx package does parse_cif_noX.py expect? HOT 2
- Global_score
- No use of GPU?
- jsonl file to pdb
- --omit_AA "CM" parameter?
- How to confirm the global polar amino acid bias value? What is the meaning of 1.39?
- No chain_set_test.jsonl file in the root directory
- Design complexes with unknown chains (proposed fix included)
- Amino acid sequence has too many "K/E" HOT 2
- How do I use a PSSM with proteinMPNN?
- Need of assistance and advising
- Model is adding an amino acid to the original sequence HOT 5
- Creates hydrophobic surface patches wit many Ala side chains HOT 2
- Training time HOT 1
- What is the difference between --conditional_probs_only_backbone and --unconditional_probs_only HOT 1
- Empty parsed_pdbs.jsonl file from parse_multiple_chains.py helper script? HOT 1
- RuntimeError: Class values must be smaller than num_classes. | protein_mpnn_utils.py & mask_size issue?
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