25. Phenix Dock in Map protocol
Protocol designed to automatically fit atomic structures to electron density maps in Scipion by using PHENIX dock in map [Liebschner et al., 2019], application that uses a convolution-based shape search with which it finds the parts of the map that are similar to the model. Additional information can be found in PHENIX documentation.
- Requirements to run this protocol and visualize results:
- Scipion plugin: scipion-em
- Scipion plugin: scipion-em-phenix
- PHENIX software suite (tested for versions 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 -> Rigid fitting (Fig. 25.1 (A))
Protocol form parameters (Fig. 25.1 (B)):
- Input map: Electron density map previously downloaded or generated in Scipion to fit the atomic structure.
- Resolution (Å): Electron density map resolution.
- Input atom structure: Atomic structure previously downloaded or generated in Scipion to be fitted to an electron density map.
- Atom structure number of copies: Number of models that have to be simultaneously fitted to an electron density map.
- 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.
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 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). Coordinate axes, map, initial unfitted model and final fitted atomic structure are model numbers #1, #2, #3 and #4, respectively, in ChimeraX Models panel.
- Summary content:
- Protocol output (below framework):phenix - dock in map -> ouputPdb;AtomStruct (pseudoatoms=True/ False, volume=True/ False).Pseudoatoms is set to True when the structure is made of pseudoatoms instead of atoms. Volume is set to True when an electron density map is associated to the atomic structure.
- SUMMARY box:No summary information