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 mutationscores command. 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 first column should describe the mutation in the format recommended by the Human Genome Variation Society (HGVS), except with 1-letter amino acid codes instead of 3-letter codes. For example, a mutation of tyrosine 392 to alanine would be described as:
p.(Y392A)
Deep mutational scans often include deletions. For example, the following denotes a deletion of valine 6:
p.(V6del)
ChimeraX currently offers no way to visualize the deletions and will ignore such lines.
Opening a mutation scores file automatically shows a scatter plot of the mutants with the first two scores as the axes, or a histogram if the file only contains one kind of score. The menus below the plot can be used to change which scores are plotted and for which mutation set.
Opening a mutation scores file automatically associates the data with a structure chain open in ChimeraX, if its sequence and residue numbering match that in the file. However, if more than one matching chain is present, the open command chain option can be used to specify which to use. Alternatively, the scores can be associated with a structure later with the mutationscores structure command.