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cyrus submit ai-folding input.fasta --mode=monomer --ai-tool=openfold

Currently, openfold does not support multichain modeling

To model a prokaryotic multichain protein with alphafold

cyrus submit Multiple fasta files can be evaluated in a single job like this:

cyrus submit ai-folding input.fasta input2.fasta --mode=monomer --ai-tool=openfold

The Openfold tool can run with either the weights trained by deepmind for alphafold, or weights trained by the AlQuarashi lab for openfold. The openfold trained weights are the default, to use the alphafold weights with the openfold tool, run

cyrus submit ai-folding input.fasta --mode=multimer monomer --ai-tool=alphafold openfold --is-prokaryotemodel-sets=alphafold

To model a eukarytotic multichain protein with alphafoldmulti-chain protein

cyrus submit input.fasta --mode=multimer --ai-tool=alphafold

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