Dock Prep Dock Prep icon

Dock Prep can perform several tasks to prepare structures as input to the DOCK suite of programs (or for other types of calculations), including:

Many of the tasks can be done separately in Chimera, but Dock Prep brings them together for convenience. Dock Prep has limitations and remains under active development. Thanks to P. Therese Lang for helping to develop this tool.

If there are extra molecules other than solvent that should not be present during docking, these should be deleted before Dock Prep is run. Dock Prep does not delete extra chains or other molecules besides solvent, because depending on the specific situation, they might be important for binding or maintaining receptor structure. Similarly, binding might require the presence of more chains than are included in the structure file; the relevant form should be generated before Dock Prep is run (see also Unit Cell).

There are several ways to start Dock Prep, a tool in the Structure Editing category (including using it via Minimize Structure).

Under Molecules to prep, the structure(s) of interest should be chosen from the list of open molecule models. Individual models or blocks of models can be chosen with the left mouse button. Ctrl-click toggles the status of an individual model. To choose a block of models without dragging, click on the first (or last) and then Shift-click on the last (or first) in the desired block.

Several operations can be performed on the chosen structures:

OK performs the specified tasks and dismisses the Dock Prep dialog, while Cancel simply dismisses the dialog. Help opens this manual page in a browser window.

Tasks are performed in the order listed on the Dock Prep dialog. If any individual step is canceled, subsequent steps will not be performed; for example, if charge assignment is canceled, a Mol2 file will not be written. To skip a particular step, uncheck its option before initiating the Dock Prep calculation.

A related tool is ViewDock, which facilitates interactive screening of DOCK output.


Does not build missing segments. Structures may have missing residues or atoms where coordinates could not be determined because of disorder or flexibility. Dock Prep can fix truncated sidechains, but it will not build missing backbone segments.

UCSF Computer Graphics Laboratory / December 2007