6. ChimeraX Restore Session protocol

Protocol designed to restore ChimeraX session, provided that this session has been saved previously in Scipion. Currently, four protocols save ChimeraX sessions when ChimeraX commands scipionwrite, scipionss or scipioncombine are used, chimerax-rigid fit, chimerax-operate, chimerax-model from template and chimerax-map subtraction (Appendices CHIMERAX Rigid fit, Operate, Model from template and Map subtraction, respectively). Restored sessions allow inspect any element contained in a previously saved ChimeraX session, perform ChimeraX operations, and finally save maps or atomic structures.

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

  Model building -> Tools-Calculators (Fig. 6.5 (A))
  

  Fig. 6.5 Protocol chimerax-restore session. A: Protocol location in Scipion menu. B: Protocol form.

• Protocol form parameters (Fig. 6.5 (B)):
  • Input section
    • Input protocols: Parameter that allows to select a particular protocol in which ChimeraX session has been saved in Scipion. As it was mentioned before, four protocols support this possibility (ChimeraX rigid fit, ChimeraX operate, ChimeraX model from template and ChimeraX map subtraction).
  • 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, session will be saved by default, without prejudice that it may be saved with scipionss command. ChimeraX sessions can be restored again by using this same chimerax-restore session protocol.
• 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.
  ChimeraX graphics window will be opened after executing the protocol showing the complete list of elements that appeared in ChimeraX graphics window when the session was saved, coordinate axes, electron density maps, and atomic structures. Steps to follow depend on the specific operation to carry out. New volumes or structures may be generated as usual in ChimeraX, and they can be combined or saved in the common way.
  • 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
    

  • To save a map or an atomic structure generated with this protocol, write 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 atomic structures and electron density volumes, the three coordinate axes are represented; X axis (red), Y axis (yellow), and Z axis (blue) (Fig. 5.3). In this particular case a ChimeraX graphics window identical to the input session will be opened and it will include every element saved lately.
• Summary content:
  • If an atomic structure is generated:
    • 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 a volume is generated:
    • Protocol output (below Scipion framework):

      chimerax - operate -> output 3D map name; Volume (x, y, and z dimensions, sampling rate).
    • SUMMARY box:

      Produced files:

      output 3D map name, starting with the prefix (.mrc file)

      we have some result