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| Code Block |
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position original_residue mutation 1 M DG 2 Q T |
Optional - multi-mutations-file
TSV file containing mutations to run simultaneously. Similar format to the mutations file, but with each run’s mutations separated with
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| Code Block |
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---
position original_residue mutation
1 M DY
---
position original_residue mutation
1 M DN |
Optional - all-mutations mode
you can omit an input mutations-file and instead run in all-mutations mode, where all mutations at each position will be selected
Optional - dump-pdb mode
run with this flag to output the PDB for each mutation as well as the score
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cyrus submit ddg <pdb-file> --all-mutations --dump-pdb |
Run DDG on an input structure with single mutations from mutations file and multi-mutations from multi-mutations file
| Code Block |
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cyrus submit ddg <pdb-file> --mutations-file <mutations-file> --multi-mutations-file <multi-mutations-file> |
Python Examples (DDG)
Run DDG on an input structure with mutations that are included in the input mutations file
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results.tsv
file with one mutation and score per-line
multi-results.tsv
file with one score per multi-mutation run
mutation-input.tsv
input mutations file
multi-mutation-input.tsv
input multi-mutations file
pdbresults.tar.gz
output PDB files, will be empty if
--dump-pdbomitted
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