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I created unpaired and paired MSAs using jackhmmer searches and created two separate MSA contexts out of them. However, when you combine protein complex modeling with a ligand, the AllAtomStructureContext determines the token size from the number of protein residues plus the ligand atoms. In my hands, this produced a "BeartypeCallHintParamViolation" since the token size for MSAContext does not account for ligand tokens. I solved this by padding my paired MSA to the expected token size but most likely there is a better way to solve this?! Would be very happy for input! Many thanks!
The text was updated successfully, but these errors were encountered:
I created unpaired and paired MSAs using jackhmmer searches and created two separate MSA contexts out of them. However, when you combine protein complex modeling with a ligand, the AllAtomStructureContext determines the token size from the number of protein residues plus the ligand atoms. In my hands, this produced a "BeartypeCallHintParamViolation" since the token size for MSAContext does not account for ligand tokens. I solved this by padding my paired MSA to the expected token size but most likely there is a better way to solve this?! Would be very happy for input! Many thanks!
The text was updated successfully, but these errors were encountered: