ChimeraX can read the results of deep mutational scanning from a mutation scores file (format name ms, filename suffix .csv) for visualization and analysis with the Mutation Scores tool and/or mutationscores command. For example, .csv files downloaded or fetched from MaveDB can be opened.
Deep mutational scanning generally involves mutating each position in a protein to all 20 standard amino acids and evaluating the large number of mutants with various high-throughput assays. The assay scores are tabulated in the file as comma-separated values. The first line of the file gives the names of the columns, and subsequent lines give the values, for example:
variants,wildtype,position,mutation,type,surface,surface_se,abundance,abundance_se,dox,dox_se,mtx,mtx_se,sn38,sn38_se p.(V6A),V,6,A,missense,0.052806582,0.311071605,0.095010571,0.391069124,-0.549746993,0.43742939,0.253708238,0.317841138,-0.373043663,0.444088911 p.(V6C),V,6,C,missense,0.132574054,0.300261964,0.129538083,0.371928707,-0.012776432,0.376829305,-0.005007274,0.220479589,0.447843883,0.270068523 [...]
The name of the column describing the mutation should be hgvs, hgvs_pro, or variants, and the column entries use protein HGVS syntax with either amino acid 3-letter codes with the first letter capitalized (as recommended by the Human Genome Variation Society) or capitalized 1-letter codes. For example, a mutation of tyrosine 392 to alanine could be given as:
p.(Tyr392Ala)
– or –
p.(Y392A)
Rows describing deletions, insertions, stop codons and multi-residue mutations are can also be specified. ChimeraX does not currently offer ways to visualize multi-residue mutations except for one or more consecutive residue deletions or insertions of multiple residues at one position.
Opening a mutation scores file automatically shows the Mutation Scores tool.