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:
Ways to restart a session:
A session may not restore correctly, or at all, in a version of Chimera
older than that used to create the session.
If a session includes a structure that has duplicate atom names within
the same residue, it will not restore correctly.
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:
Regardless of whether pre-existing models are closed when a
session is restored, any pre-existing
will be removed, while pre-existing
sequence alignments will be retained.
can be used to apply the transformation of one model to another
can be used to restore default or previously saved positions
What Sessions Include
The following are saved in session files:
- display status, colors, and styles
of atoms, bonds, pseudobonds,
- atomic coordinates, including alternate locations and changes such as from
- PDB headers and residue secondary structure assignments
- atomic B-factor (isotropic and anisotropic),
Measurements including axis, plane, and centroid representations
- trajectory frames that had been
prior to saving, and if all frames, the
- 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
including regions, associations, and trees
- standard labels, status of
- window size, model translation/rotation, and global scale
- clipping plane
status, locations, and orientations
- saved positions
- color definitions (see
and aliases (see alias)
- selections, current and saved
(except of surface models)
- viewing parameters:
center of rotation method,
- camera mode and
(however, the camera mode will not be restored if it is
or if Chimera was already in
prior to session restoration)
- Blast Protein results,
ModBase Model List,
CASTp Pocket List
- status, information, and/or models from
- session thumbnail image and notes, if any, from using
Save Session As and/or
- the status of many other tools
- preferences settings
preferences file can be changed between saving and restarting
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)
UCSF Computer Graphics Laboratory / February 2013