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Joseph Watsonnrbennet
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correct example
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examples/design_ppi_flexible_peptide_with_secondarystructure_specification.sh

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# We then specify that we want this to adopt a helical conformation
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# If you wanted to specify that it should adopt a strand conformation, you would specify `contigmap.inpaint_str_strand`
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../scripts/run_inference.py inference.output_prefix=example_outputs/design_ppi_flexible_peptide_with_secondarystructure inference.input_pdb=input_pdbs/tau_peptide.pdb 'contigmap.contigs=[70-100/0 B165-178]' inference.num_designs=10 'contigmap.inpaint_str=[B165-178]' scaffoldguided.scaffoldguided=True 'contigmap.inpaint_str_strand=[B165-178]'
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../scripts/run_inference.py inference.output_prefix=example_outputs/design_ppi_flexible_peptide_with_secondarystructure inference.input_pdb=input_pdbs/tau_peptide.pdb 'contigmap.contigs=[70-100/0 B165-178]' inference.num_designs=10 'contigmap.inpaint_str=[B165-178]' scaffoldguided.scaffoldguided=True 'contigmap.inpaint_str_helix=[B165-178]'

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