Chimera Sessions

A Chimera session (the state of Chimera during use) can be saved and restored. A session file consists of Python code that reconstitutes most aspects 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
• with File... Open (file type Python)
• with the command open (file type Python)

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.

The following are saved in session files:

• display status, colors, and styles of atoms, bonds, ribbons, and molecular surfaces
• atomic coordinates, including alternate locations and changes such as from bond rotation
• status of other model types: (nonmolecular) surface, volume and VRML (except a VRML model opened from a file that is then moved before the session is saved)
• window size, model translation/rotation, and global scale
• positions of clipping planes, global and per-model; per-model slab thickness
• viewing parameters: depth cueing, subdivision quality, silhouettes, 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)
• standard labels and 2D Labels
• pseudobonds, including distance monitors
• PDB headers and residue secondary structure assignments
• atomic B-factor (isotropic and anisotropic), occupancy, radius, and charge values
• attributes created with Define Attribute
• 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
• information from Surface Capping, Surface Color, Surface Zone, and Color Zone
• the status of Rotamers, Volume Viewer, Volume Tracer, Multiscale Models, Scale Bar, and ViewDock
• sequence alignments open in Multalign Viewer and their regions and associations

• the status of many other tools such as 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)