Sessions

A Chimera session (the state of Chimera during use) can 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.

Ways to save a session:

• 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 (binary) with the same name except *.pyc instead of *.py. The binary speeds up session restoration and will be used (if present) even when the *.py file has been specified. Further, opening the *.pyc file directly will start the session even if the *.py file has been deleted. However, keeping the *.py file is recommended:

• the *.py file will work with subsequent versions of python, whereas the *.pyc file will only work with the same version of python that generated it
• the *.py file can be viewed and edited with a text editor, whereas the binary *.pyc file cannot
• a method that preserves binary information must be used to transfer *.pyc files between computers, whereas *.py files can be transferred as plain text

Information that is saved includes:

• the display status of molecule models and molecular surface (MSMS) models and their subparts, translation/rotation and scale, representations, and colors
• molecular coordinates, including modifications/additions (such as from performing bond rotations or using swapaa or AddH)
• VDW radii (even if changed from default values)
• PDB headers, secondary structure assignments, B-factor and occupancy values
• labels (standard and 2D Labels)
• 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
• positions of the global clipping planes (those shown in the Side View) and of any per-model clipping planes and slabs; per-model slab thickness
• viewing parameter settings: depth cueing, subdivision quality, projection mode, center of rotation method, lighting, shininess/brightness
• information from Surface Capping, Surface Color, Surface Zone, and Color Zone
• the status of Volume Viewer, Volume Path Tracer, Multiscale Models, Scale Bar, and ViewDock
• 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
• 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)