SimpleSession

SimpleSession allows many aspects of the state of Chimera during modeling (a session) to be saved and restored. A session file consists of Python code that reconstitutes the state of Chimera by displaying data and performing other operations.

Molecular coordinate and sequence alignment data are included in the session file; however, volume data files must still be present to restart a session in which they were open. When a session with volume data is restarted, the user may be queried about file location(s) if the data or the session file have been moved since the session was saved.

There are several ways to start SimpleSession, a tool in the Utilities category. Starting SimpleSession opens a dialog for saving the session file.

Other ways to save a session all use the SimpleSession functionality:

• File... Save Session
• File... Save Session As...
• the command

  save session_name

• opening the Python file session_name.py directly, like other types of input
• the command

  load session_name
  -OR-
  load session_name.py

In the future, a more complete session-saving mechanism will be available. Information that is saved includes:

• the display status of molecule and surface models and their subparts, translation/rotation and scale, labels, representations, and colors (except for custom surface colors)
• molecular coordinates, including modifications/additions (such as from performing bond rotations or using swapaa or AddH)
• color definitions (see colordef)
• saved positions (see savepos; positions saved explicitly plus the position at the time of the save, named session-start)
• selections (current and saved)
• pseudobonds, including distance monitors
• window size
• clipping plane positions (except sessions saved with Chimera Alpha version 1 build 1351)
• viewing parameter settings: depth cueing, subdivision quality, projection mode, center of rotation method
• the status of Volume Viewer, Volume Path Tracer, and Scale Bar
• sequence alignments open in Multalign Viewer and their regions and associations

• VRML models
• changes in VDW radii
• custom surface colors (such as surface coloring according to electrostatic potential by DelPhiViewer)
• the status of most tools, including the Command Line and Side View
• preferences settings (the preferences file can be changed between saving and restarting a session)
• which preferences file is being used (an issue when there are different preferences files in different locations and a session file has been moved from its original location)