[Chimera-users] editing Python saved sessions

Thomas Goddard goddard at cgl.ucsf.edu
Mon May 22 20:41:41 PDT 2006

Hi Jonathan,

  I would guess your session files for virus capsids are large due to
having alot of atoms because you have loaded many copies of the capsid
protein molecule.  If this is the case than Eric's suggestion to use
the latest Chimera snapshot (1.2224) is your best bet.  The only other
options being to save fewer atoms, or use a machine with more memory.
You can create the *.pyc file on a different machine with more memory
that need not have interactive graphics and transfer it back to your
visualization machine if necessary.  The *.pyc file is platform
independent (windows, mac, linux, sgi, ...).

  Another possible cause of large session files is if you are looking
at virus models with a large number of chains.  For instance I made a
model of a crystal lattice of 50 copies of a small virus (satellite
tobacco mosaic virus, 1a34) with asymmetric unit having 6 chains.
That gave (50 capsids) x (60 asym units per capsid) x (6 chains per
asym unit) = 18000 chains.  The session file was about 19 Mb.  There
were only 3500 atoms loaded (just one asym unit) and the space in the
session file for that was negligible.  So the session file chews up
about 1 Mbyte per 1000 multiscale chains.  Unless you are making some
extremely large molecular assemblies your sessions are probably mostly
filled with atom data, not multiscale chain data.

  Thanks for making the Science cover image!  I am interested in
making virus architecture movies in Chimera.  Here is an example using
my current favorite capsid, orthoreovirus PDB 2cse:


It is in the Chimera animation gallery



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