24. Phenix Superpose PDBs protocol

Protocol designed to superpose two atomic structures in Scipion by using phenix.superpose_pdbs program [Zwart et al., 2017]. Integrated in the PHENIX software suite, PHENIX protocol phenix-superpose pdbs allows to compare visually the geometry of two atomic structures by overlapping them. Root mean square deviation (RMSD) between fixed and moving structures is computed before and after the superposition.

  • Requirements to run this protocol and visualize results:
    • Scipion plugin: scipion-em
    • Scipion plugin: scipion-em-phenix
    • PHENIX software suite (tested for versions 1.13-2998, 1.16-3549, 1.17.1-3660, 1.18.2-3874, 1.19.2-4158 and 1.20.1-4487)
    • Scipion plugin: scipion-em-chimera
  • Scipion menu:
    Model building -> Tools-Calculators (Fig. 24.1 (A))
    Protocol **phenix-superpose pdbs**. A: Protocol location in *Scipion* menu. B: Protocol form.

    Fig. 24.1 Protocol phenix-superpose pdbs. A: Protocol location in Scipion menu. B: Protocol form.

  • Protocol form parameters (Fig. 24.1 (B)):

    • Fixed atomic structure: Fixed PDBx/mmCIF, previously downloaded or generated in Scipion, to which the moving one will be aligned.
    • Moving atomic structure: PDBx/mmCIF, previously downloaded or generated in Scipion, that will be aligned to the fixed one.
  • Protocol execution:
    Adding specific moving_structure/fixed_structure 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 and ChimeraX graphics window will be opened by default. Atomic structures and volumes are referred to the origin of coordinates in ChimeraX. To show the relative position of atomic structure and electron density volume, the three coordinate axes are represented; X axis (red), Y axis (yellow), and Z axis (blue) (Fig. 5.3).

  • Summary content:

    SUMMARY box:
    RMSD between fixed and moving atoms (start and final values).