[Chimera-users] PDB data

Eric Pettersen pett at cgl.ucsf.edu
Tue Mar 31 15:43:14 PDT 2009

On Mar 31, 2009, at 3:03 PM, Matthew Dougherty wrote:

> Normally when Chimera saves a session it includes the PDB data as part
> of the session file.
> Is there a way to prevent that and have the individual pdb models
> saved as PDB files?

The short answer is no.

Chimera originally preserved molecular data as embedded PDB files in  
it's session files (embedded as strings).  Over time it became clear  
that this was problematic because a) PDBs are pretty verbose and slow  
to parse, and b) some molecular data is just problematic to store in  
PDB format.  In particular, the 5-digit limit for atom serial numbers  
in CONECT records is a deal breaker.  So two and a half years ago  
(1.2304 release) the embedded-PDB-file approach was abandoned and the  
data was simply stored as Python lists and dictionaries.  This  
resulted in smaller session files with faster restore times and less  
memory use.  We anticipate using Python's pickle mechanism to further  
reduce restore times and memory use (during the .pyc compile) in the  
next release.  So the only part of the PDB file preserved more or less  
intact is the header lines (as a dictionary of lists of strings).  So  
the long answer is also no!



                         Eric Pettersen
                         UCSF Computer Graphics Lab

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