7. ChimeraX Rigid Fit protocol

Protocol designed to manually fit atomic structures to electron density maps in Scipion by using ChimeraX. If map and model are quite close, e.g. after running PHENIX dock in map protocol, automatic fitting is also possible. Fitted atomic structures generated by using this protocol can be saved in Scipion after executing specific ChimeraX commands.

• Requirements to run this protocol and visualize results:
  • Scipion plugin: scipion-em
  • Scipion plugin: scipion-em-chimera
• Scipion menu:

  Model building -> Rigid fitting (Fig. 7.14 (A))
  

  Fig. 7.14 Protocol chimerax-rigid fit. A: Protocol location in Scipion menu. B: Protocol form.

• Protocol form parameters (Fig. 7.14 (B)):
  • Input section
    • Input Volume: Mandatory param to load the electron density map previously downloaded or generated in Scipion to fit the atomic structure.
    • Input additional Volumes: Idem. If additional maps, others than the previous map, are needed.
    • Atomic structure to be fitted: Mandatory param to load the atomic structure previously downloaded or generated in Scipion to be fitted to an electron density map.
    • Other reference atomic structures: Atomic structures others than the previous model used to help in the rigid body fitting process.
  • Help section
    This section contains ChimeraX commands required to save models according to their reference volumes, which can also be saved if required. Remark that using scipionwrite command, ChimeraX session will be saved by default, without prejudice that it may be saved with scipionss command. ChimeraX sessions can be restored by using chimerax-restore session protocol. In addition, scipioncombine allows to combine several atomic structures in a unique model.
• Protocol execution:
  Adding specific map/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.
  ChimeraX graphics window will be opened after executing the protocol. The electron density map and the atomic structure are shown. Main steps to complete the rigid body fitting are:
  • If density map and atomic structure are quite close to each other:
    Go to ChimeraX main menu and select Tools -> Volume Data-> Fit in Map. A small Fit in Map window will be opened. Once the right atomic structure and the electron density volume have been selected, fit them by clicking Fit.

    Note: The same result can be obtained by typing in the command line fit #n1 inMap #n2, with #n1 and #n2 model numbers of model and map.

  • If model and map are far from each other, start the fitting process interactively activating and inactivating ChimeraX objects alternatively to finally get map and model close enough to go to the previous step. Otherwise, consider the possibility of running the protocol chimerax-rigid fit after PHENIX dock in map protocol.

  • To combine two or more atomic structures, write in ChimeraX command line:

    scipioncombine #n1,n2
    

    #n1 and #n2 are the respective model numbers of two different atomic structures. Optionally you can set the model number of the output combined structure #n3:

    scipioncombine #n1,n2 modelid n3
    

  • Save fitted model by writing in ChimeraX command line:

    scipionwrite #n prefix userString_
    

    Replace #n by model numbers shown in ChimeraX Models panel. prefix + string preferred by the user to easily identify the atomic structure is optional, although quite recomendable.
  • Close ChimeraX graphics window.
• 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 model and map, the three coordinate axes are represented; X axis (red), Y axis (yellow), and Z axis (blue) (Fig. 5.3). Coordinate axes, map, and atomic structure are model numbers #1, #2, and #3, respectively, in ChimeraX Models panel in the most simple case.
• Summary content:
  • If only the atomic structure has been saved by scipionwrite command:
    • Protocol output (below Scipion framework):

      chimerax - operate -> output atomic structure name, starting with the prefix;

      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:

      Produced files:

      output atomic structure name, starting with the prefix (.cif file)

      we have some result
  • If both the atomic structure and its reference electron density map have been saved by scipionwrite command:
    • Protocol output (below Scipion framework):

      chimerax - rigid fit -> Map_name; Volume (x, y, and z dimensions, sampling rate).

      chimerax - rigid fit -> Atom_struct_name;

      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:

      Produced files:

      Map_name file, starting with the prefix (.mrc)

      we have some result