5. Phenix Dock and Rebuild protocol

PHENIX-based protocol designed to dock and rebuild AlphaFold2 [Jumper et al., 2021], RoseTTAFold [Baek et al., 2021] and other predicted models in Scipion. According to PHENIX documentation the tool dock_and _rebuild combines the functions of processing, docking and rebuilding predicted models into a cryo EM map. The three previous steps can be run also one by one using specific protocols for processing, docking and rebuilding. The shorter way of the combined dock_and_rebuild procedure is more convenient for simple cases. If the result does not seems goood enough, you may always run the three steps individually. Identically, you can start with the whole map as input, or using a manually segmented part of the map and working with the asymmetric unit (see also appendix Extract asymmetric unit).

  • 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 -> Flexible fitting (Fig. 5.5 (A))
    Protocol **phenix-dock and rebuild predicted model**. A: Protocol location in *Scipion* menu. B: Protocol form.

    Fig. 5.5 Protocol phenix-dock and rebuild predicted model. A: Protocol location in Scipion menu. B: Protocol form.

  • Protocol form parameters (Fig. 5.5 (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).
  • 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, and dock-and-rebuilt model (suffix .pdb) are model numbers #1, #2, #3, and #4, 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: