Dock Prep performs several tasks to prepare structures for DOCK or for other calculations, such as:
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:
- selenomethionine (MSE) to methionine (MET) - change MSE residues to MET by changing the selenium atom to a sulfur atom named SD and adjusting the CG-SD and SD-CE bond lengths to 1.81 and 1.78 Å, respectively
- bromo-UMP (5BU) to UMP (U) - change 5-bromouridine-5'-monophosphate (PDB chemical component 5BU) to RNA residue uridine-5'-monophosphate (U) by deleting the bromine atom
- methylselenyl-dUMP (UMS) to UMP (U) - change 2'-methylselenyl-2'-deoxyuridine-5'-phosphate (PDB chemical component UMS) to RNA residue uridine-5'-monophosphate (U) by replacing the methylselenyl moiety with an oxygen atom named O2' and adjusting the bond length to 1.430 Å
- methylselenyl-dCMP (CSL) to CMP (C) - change 2'-methylselenyl-2'-deoxycytidine-5'-phosphate (PDB chemical component CSL) to RNA residue cytidine-5'-monophosphate (C) by replacing the methylselenyl moiety with an oxygen atom named O2' and adjusting the bond length to 1.430 Å
The rotamer library options replace each truncated sidechain with a complete sidechain of the same residue type, as if using the command swapaa with the specified rotamer library, preserve true, and ignoreOtherModels true (default settings of other options). If different settings are desired, use swapaa separately before using Dock Prep. The mutation option changes each residue with a truncated sidechain to glycine or alanine, the latter if a CB atom is present.
Using one of these options to generate complete sidechains is recommended because in incomplete residues, the partial charges will not sum to integer values, and extra hydrogens (unrecognized in the charge addition step) will be added where the missing atoms would have been attached.
Potentially ambiguous or rare (shifted-pKa) protonation states, especially in binding sites and nonstandard residues, should be verified and corrected before charges are assigned. For example, extra hydrogens can be deleted, and atom types can be edited (before hydrogen addition) with setattr or Build Structure.
Charges for standard residues (water, standard amino acids, standard nucleic acids, and a few common variants and capping groups) are taken from Amber (details). If any atoms in standard residues are not recognized, a warning will appear and information on the atoms will be sent to the Reply Log. Cases of unrecognized atoms in standard residues and/or incorrect net charges should be examined and resolved.
Charges for nonstandard residues, if any, are calculated using Amber's Antechamber module (included with Chimera; publications involving its use should cite the reference). It is necessary to specify the formal charge of each nonstandard residue and which charge calculation method should be used.
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.