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uw-ipd / RoseTTAFold2NA

RoseTTAFold2 protein/nucleic acid complex prediction
MIT License
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RoseTTAFold2NA support multi-chain PDB output #39

Closed lipan6461188 closed 3 months ago

lipan6461188 commented 1 year ago

I have some modifications on RoseTTAFold2NA (main brach):

  1. Add "-parse_seqids" to makeblastdb;
  2. Change "-M 5000" to "-M 0" (cd-hit-est) and add "-M first" (hhfilter) to disable error during generating RNA MSA;
  3. network/parsers.py: Use table_na to filter nucleotide not in ('A', 'T', 'C', 'G', 'U', 'D', 'N'), otherwise the program will crash;
  4. network/predict.py: Add chain_index and residue_index to support multi-chain PDB output.
amorehead commented 1 year ago

Are there any updates on merging this into main? This seems like a useful PR to have integrated into the codebase. Or have all the main changes in this PR already been merged into main by @fdimaio?

fdimaio commented 1 year ago

Hello,

This functionality should be present in the current version of RF2na (the patch was incompatible with some other changes that had been made)