design_motifscaffolding_inpaintseq.sh

#!/bin/bash
# Here, we're running one of the motif-scaffolding benchmark examples
# Specifically, we're scaffolding site 5 from RSV-F protein
# This is equivalent to the example in design_motifscaffolding.sh, except that we're adding the contigmap.inpaint_seq flag
# The logic here is that only some of the amino acids are important for the function of the motif, and others can be redesigned.
# This can promote better packing, as RFdiffusion is not forced to pack against specific (but unimportant) residues on the back-side of the motif  
# We specify the output path and input pdb (the RSV-F protein)
# We specify the protein we want to build, with the contig input:
#   - 10-40 residues (randomly sampled)
#   - residues 163-181 (inclusive) on the A chain of the input
#   - 10-40 residues (randomly sampled)
# We generate 10 designs
# We then specify that residues 163-168 (inclusive), 170-171 (inclusive) and 179 (inclusive) on the A chain of the input, should be masked in the input

../scripts/run_inference.py inference.output_prefix=example_outputs/design_motifscaffolding_inpaintseq inference.input_pdb=input_pdbs/5TPN.pdb 'contigmap.contigs=[10-40/A163-181/10-40]' inference.num_designs=10 'contigmap.inpaint_seq=[A163-168/A170-171/A179]'