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:

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

• with File... Restore Session
• with the command load
• by directly opening the session file (Python, *.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
• while *.py files are transferable among different types of computers, *.pyc files generated on one system may not be read correctly on another

If models are already open when a session file is read, a user will be given the option to close the existing session (models and other data) before restoring the session from the file. Otherwise, the sessions will be merged.

When sessions are merged, models in the incoming session will be assigned new ID numbers. Regardless of how models were moved beforehand, a session will always restore in the position in which it was saved. It may be helpful in some cases to reset model positions right before merging in a session. Models opened from individual data files can be reset to their original positions with the command reset (without arguments). Models restored from a session file can be reset to their positions when the session was saved with reset session-start.

Session files include the following kinds of information:

• the display status of molecule models and molecular surface (MSMS) models and their subparts, translation/rotation and scale, display styles, 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
• 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 clipping planes, global and per-model; per-model slab thickness
• viewing parameters: depth cueing, subdivision quality, silhouette edges, projection mode, center of rotation method, lighting, shininess/brightness
• camera mode and stereo parameters (however, the camera mode will not be restored if it is sequential stereo, or if Chimera was already in sequential stereo prior to session restoration)
• 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)