3. Phenix Dock Predicted Model protocol

PHENIX-based protocol designed to dock processed AlphaFold2 [Jumper et al., 2021], RoseTTAFold [Baek et al., 2021] and other predicted models in Scipion. According to PHENIX documentation the tool dock_predicted_model uses the connectivity of the model as a restraint so that the docked domains are in a reasonable arrangement. Although the method has been designed to handle with symmetry, you can get usually a better result segmenting manually the map and working with the asymmetric unit (see also appendices Extract asymmetric unit and Phenix Dock in Map). Each domain is docked and refined by rigid-body refinement. When all the domains are docked, the residues are sorted and a single chain is produced.

  • Requirements to run this protocol and visualize results:
    • Scipion plugin: scipion-em
    • Scipion plugin: scipion-em-phenix
    • PHENIX software suite (tested for version 1.20.1-4487)
    • Scipion plugin: scipion-em-chimera
  • Scipion menu: Model building -> Rigid fitting (Fig. 3.4 (A))
    Protocol **phenix-dock predicted model**. A: Protocol location in *Scipion* menu. B: Protocol form.

    Fig. 3.4 Protocol phenix-dock predicted model. A: Protocol location in Scipion menu. B: Protocol form.

  • Protocol form parameters (Fig. 3.4 (B)):
    Input section:
    • Predicted AlphaFold2 model: Any atom structure that the user would like to process. It can be generated as AlphaFold2 prediction through the Scipion protocol chimerax-alphafold prediction (See Appendix AlphaFold2 Initial Model Prediction) or generated outside Scipion. In this last case, the predicted atom structure has to be imported previously (look at Appendix Import atomic structure).
    • Processed AlphaFold2 model: Since the protocol phenix-dock predicted model is usually the second step in the modeling workflow of AlphaFold2 predictions, it uses the previous processed prediction model, in which all the uncertain residues have been trimmed and the rest of the sequence has been grouped in compact domains. Then, include here the output of the protocol phenix-dock predicted model (see appendix Process Predicted Model).
    • Input map: Electron density map previously downloaded or generated in Scipion to fit the atomic structure.
    • High-resolution limit (Å): Electron density map resolution.
    • Number of threads: Advanced param. Depending on the size of map and model, and the number of models to fit the process could be quite slow and you can accelerate it by increasing the number of threads.
    • Extra Params: Advanced param. Look at PHENIX documentation page to include additional params with the appropriate syntaxis.

  • Protocol execution:

    Adding specific protocol label is recommended in Run name section, at the form top. To add the label, open the protocol form, press the pencil symbol at the right side of Run name box, complete the label in the new opened window, press OK and, finally, close the protocol. This label will be shown in the output summary content (see below). If you want to run again this protocol, do not forget to set to Restart the Run mode.
    Press the Execute red button at the form bottom.
  • Visualization of protocol results:
    After executing the protocol, press Analyze Results in the Scipion framework and the ChimeraX graphics window will be opened. Atomic structures and volumes are referred to the origin of coordinates in ChimeraX. To show the relative position of atomic structures and electron density volume, the three coordinate axes are represented; X axis (red), Y axis (yellow), and Z axis (blue) (Fig. 5.3). Coordinate axes, map, initial predicted model, processed unfitted model (suffix .pdb) and final fitted atomic structure (suffix .pdb.pdb) are model numbers #1, #2, #3, #4 and #5, respectively, in ChimeraX Models panel. Initial model residues predicted by AlphaFold2 are colored according to the alphafold bfactor (LDDT values) palette of ChimeraX (model #3).
  • Summary content: