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

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

  load session_name
  -OR-
  load session_name.py

Opening a session file creates a compiled version of the file, given the same name except *.pyc instead of *.py. The presence of the compiled version speeds up session restoration. Since the compiled (*.pyc) file contains complete session information, opening it will start the session even when the *.py file has been deleted. One disadvantage of the compiled session file, however, is that unlike the uncompiled version, its contents cannot be viewed and edited with a text editor.

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

• the display status of molecule and molecular surface (MSMS) models and their subparts, translation/rotation and scale, representations, and colors (including custom surface colors, such as MSMS surface colors set by DelPhiViewer)
• molecular coordinates, including modifications/additions (such as from performing bond rotations or using swapaa or AddH)
• PDB headers, secondary structure assignments, B-factor and occupancy values
• labels and label font
• ribbon scaling, style, and residue class
• VRML models (see exceptions)
• color definitions (see colordef) and aliases (see alias)
• 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, lighting, shininess/brightness
• the status of Multiscale Models, Volume Viewer, Volume Path Tracer, and Scale Bar
• sequence alignments open in Multalign Viewer and their regions and associations

• a VRML model that originated from a file, when the file is not in its original place when the session is saved
• changes in VDW radii
• 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)