Dock Prep Dock Prep icon

Dock Prep performs several tasks to prepare structures for DOCK or for other calculations, such as:

Many of these steps can be performed separately in Chimera, but Dock Prep unites them for convenience. Thanks to P. Therese Lang (DOCK development team, see references) for helping to develop this tool. See also: PDB2PQR, ViewDock, AutoDock Vina, Write DMS, Sphgen sphere files

If extra molecules such as ligands or additional subunits are present but unwanted during docking, these should be deleted before Dock Prep is used. Dock Prep does not delete such molecules (other than water and certain ions, optionally) because they could be important for binding or for maintaining receptor structure. Conversely, the biologically relevant form of the receptor may contain more subunits than are present in the structure file. If important for downstream calculations, the relevant form should be generated before Dock Prep is run. For obtaining multimers, see: fetching PDB-biounit and PQS files, the command sym, Multiscale Models, 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:

Change - convert modified residues to standard residues for which parameters are available:
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.


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.


The following describe aspects of Dock Prep and exemplify its use in docking applications:
UCSF Computer Graphics Laboratory / November 2015