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Tool: ViewDockX

ViewDockX is a tool for the interactive analysis of molecular docking results. Users can click through a list of docked compounds (or different poses of the same compound) to view them individually in the context of a binding site. Results can be sorted, rated, and saved, and scores or other numerical descriptors can be plotted. See also: hbonds, clashes, an example file of compounds docked to H-ras (the protein part of PDB entry 121p)

Currently supported formats are Mol2 files from UCSF DOCK v4-6 and GOLD.

After one or more files of docking results have been opened, a table listing the different compounds or poses can be shown by choosing ViewDockX from the Tools menu or by using the command:

– or –
viewdockx  docked-compound-models

...the latter to limit the table to only a subset of the docked compound models currently open. The ViewDockX table and associated plots can be manipulated like other panels in ChimeraX (more...).

ViewDockX Table

In the table of docking results, the rows are different compounds or different positions of a compound, and the columns show additional data read from the input, typically including compound names and docking scores. The first two columns are generated automatically:

Any additional columns that appear when ViewDockX is first started reflect information read from the input file(s).

One or more docked compounds can be shown in the graphics window (and the rest in the table hidden) by choosing their rows in the table with the mouse. Chosen rows are highlighted in yellow. A contiguous block of rows can be chosen with click-drag, and Ctrl-click (Cmd-click on Mac) toggles a row between chosen and not chosen. When multiple compounds are chosen, changing the star rating of one also changes it for the others, in parallel.

Specific columns can be hidden/shown by clicking the bar across the top of the table (“N columns displayed...”) and using the resulting checkbox menu. Clicking the header of a column sorts by the values in that column, and a multi-column sort can be performed by clicking one header and Shift-clicking one or more additional headers. Column widths can be adjusted by dragging the vertical dividing lines.

Buttons above the table:

ViewDockX table status is saved in sessions, including which columns are shown and which rows are chosen, but not window size or location.

Graphs and Plots

Multiple graph/plot windows can be shown for the same set of docking results.

Clicking the Graph button near the top left of the ViewDockX table allows plotting all compounds along the X-axis versus one or more numerical descriptors on the Y-axis. One of the numerical descriptors can be chosen for the Sort order, and all or a subset of them as values to Graph. The data can also be shown as a histogram with specified number of bins.

Clicking the Plot button near the top left of the ViewDockX table opens another window for plotting numerical descriptors versus each other. Up to two plots can be shown in the same window, with numerical descriptors chosen for the X and Y axes of each.

A “halo” around a plotted point indicates that the compound is currently shown in the graphics window. Pausing the cursor over a plotted point shows the compound's descriptor values. Clicking a plotted point or histogram bar shows the corresponding compound(s) in the graphics window and hides the others.

UCSF Resource for Biocomputing, Visualization, and Informatics / April 2019