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 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 should use 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 and multi-residue mutations are ignored.
Opening a mutation scores file automatically shows the Mutation Scores tool.
By default, mutation scores are automatically associated with each open structure chain that has exactly the same sequence and residue numbering (as in the mutation data) the first time some analysis action is performed, such as interacting with a plot. However, specific structure chains to associate can be designated with the chains option of the open command at the time of opening the mutation data, or later (after opening the data) with mutationscores structure.