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:

• File... Save Session
• File... Save Session As... (allows saving an associated thumbnail image and session notes)
• the command save

• File... Restore Session... (clicking a session name in the file browser shows its associated thumbnail image and session notes, if any)
• File... Open... (file type Python)
• the command open (file type Python)

Restoring a session 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 is being restored, the user will be asked whether the pre-existing models should be closed. If not, the sessions will be merged; data from the incoming session will be opened, but its environmental settings such as background color and effects will not be applied.

When sessions are merged, models in the incoming session will be assigned new ID numbers and transformed so that the model with the lowest ID in the incoming session will have the same transform as the pre-existing lowest-ID model. If these transformations are not as desired, they can be adjusted:

• matrixcopy can be used to apply the transformation of one model to another
• reset can be used to restore default or previously saved positions

The following are saved in session files:

• display status, colors, and styles of atoms, bonds, pseudobonds, ribbons, and molecular surfaces
• atomic coordinates, including alternate locations and changes such as from bond rotation
• PDB headers and residue secondary structure assignments
• atomic B-factor (isotropic and anisotropic), occupancy, radius, and charge values
• attributes created with Define Attribute
• Nucleotides and Thermal Ellipsoids representations
• Structure Measurements including axis, plane, and centroid representations
• trajectory frames that had been read in prior to saving, and if all frames, the MD Movie controller dialog
• 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)
• sequence data in Multalign Viewer, including regions, associations, and trees
• standard labels, status of 2D Labels, Color Key, and Scale Bar
• window size, model translation/rotation, and global scale
• clipping plane status, locations, and orientations
• saved positions
• saved scenes and Animation timeline contents
• color definitions (see colordef) and aliases (see alias)
• selections, current and saved (except of surface models)
• viewing parameters: depth cueing, subdivision, 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)
• Blast Protein results, ModBase Model List, CASTp Pocket List
• status, information, and/or models from Cage Builder, Color Zone, Icosahedron Surface, Metal Geometry, Multiscale Models, Rotamers, Surface Capping, Surface Color, Surface Zone, ViewDock, Volume Tracer, Volume Viewer
• session thumbnail image and notes, if any, from using Save Session As and/or Notepad

• the status of many other tools
• 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)