Command: modelcif

Usage:
modelcif pae  model-spec  [ metricName  name ] [ defaultScore  s ] [ jsonOutputPath  filename ] [ palette  palette ] [ range  low,high | full ]

The modelcif pae command reads and plots pairwise (residue-residue) scoring metrics for theoretical structures from the ModelArchive database using the AlphaFold Error Plot tool. Many thanks to Gerardo Tauriello for contributing the file-reading code. See AlphaFold Error Plot for details of interacting with the plot. See also: alphafold pae

Currently, plotting does not work for ModelArchive structures that contain any residues other than standard amino acids and nucleic acids.

Some of the entries in the ModelArchive have associated pairwise reliability scores such as predicted aligned error (PAE), and multiple different metrics may be available for a given structure. In ChimeraX, the workflow to plot such a score is to:

1. fetch the ModelArchive structure of interest by its identifier in that database, for example:

   open ma-bak-cepc-0944 from modelarchive

2. use the modelcif pae command to plot pairwise scores for the already opened model, for example:

   modelcif pae #1 metricName "contact probability" defaultScore 0 palette rainbow range 0,1

The metricName option specifies the name of the pairwise metric, as given in the mmCIF ma_qa_metric table. If no name is supplied, ChimeraX looks for "PAE," and if that is not found, uses the first metric in the file.

The defaultScore s is the value to assign to any residue-residue pairs without a value for the metric in the file (default 100).

By default, the pairwise scores are written to a temporary .json file and passed to the alphafold pae command for plotting. The jsonOutputPath option allows saving the json file to a specified location, where filename is the desired pathname or the word browse to specify it interactively in a file browser window.

The default palette for coloring the PAE plot is pae, with colors assigned to values as follows:

Another palette with value range suitable for PAE plots is paegreen:

Although these palettes include value-color pairs, it may be helpful to give a value range if a colors-only palette is used instead (default 0,30). A range can also be used to override the values in a value-color palette, instead spacing the colors evenly across the specified range.

Although opening a ModelArchive structure and plotting its scores can be done with a single command,

open ma-bak-cepc-0944 from modelarchive pae true

...the modelcif pae command allows more control over which score of multiple available is plotted and how the plot is initially colored.