Comments (2)
imSeaton
commented on July 22, 2024
你好呀，感谢你的ProtSSN和洪亮团队的其他工作。
他的parse_cif_noX.py处理后用的chain_ID是asym_chain_ID，相当于PDB官方给的ID，而你说的4mxw.R这里的“R”是结构生物学家存入PDB中的author_chain_ID（可能也是CATH文件中用的chain_ID系统）。当然两者之间的转换也简单。
这个parse_cif_noX.py中data.getObj('pdb_poly_seq_scheme'）附近就有author_chain_ID --> asym_chain_ID之间的映射处理。我猜想你反过来搞个字典映射下就能把数据转成你想要的author_chain_ID形式了。希望对你有帮助。
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tyang816
commented on July 22, 2024
你好呀，感谢你的ProtSSN和洪亮团队的其他工作。 他的parse_cif_noX.py处理后用的chain_ID是asym_chain_ID，相当于PDB官方给的ID，而你说的4mxw.R这里的“R”是结构生物学家存入PDB中的author_chain_ID（可能也是CATH文件中用的chain_ID系统）。当然两者之间的转换也简单。 这个parse_cif_noX.py中data.getObj('pdb_poly_seq_scheme'）附近就有author_chain_ID --> asym_chain_ID之间的映射处理。我猜想你反过来搞个字典映射下就能把数据转成你想要的author_chain_ID形式了。希望对你有帮助。
谢谢呀，感谢你的帮助，时间有点久了我有点忘了都..我后来好像通过maxit软件曲线救国解决了这个问题
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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 1
- Global_score
- No use of GPU?
- Training model
- Retrieve per-position scores or score a chain in the context of another
- whether to redesign low confidence aas
- 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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