[Chimera-users] PDB

Eric Pettersen pett at cgl.ucsf.edu
Wed Jun 23 13:47:31 PDT 2010

On Jun 23, 2010, at 12:48 PM, Dougherty, Matthew T wrote:

> Hi,
> When PDF files are read by Chimera and the session is written, the  
> PDB data becomes part and parcel with the session files.  That is,  
> Chimera does not go back to the PDB files when it reloads the  
> session, it uses the PDB data within the session file instead; as  
> contrasted to density volume files, which are referenced by the  
> session file, and the density volume files reloaded when the session  
> file is read by Chimera.
> Is there a way to force the session file not to save the PDB  
> internally to the session file, and instead reference and interact  
> with it similar to the way volume files are managed?

Hi Matthew,
	Briefly: no.  For a variety of reasons:

1) Structural data didn't necessarily come from PDB files.
2) What to do about structure deletions and additions?
3) Session is less transportable/publishable (also occurs with volume  
files separate from sessions)

I don't see any upside really.  You wouldn't be able to swap in a  
different PDB file because there would structure attributes stored in  
the session file (charges, conservation scores, etc.) that would need  
to be mapped on a 1-for-1 basis with atoms/residues of the original  
PDB file.  I guess if your PDB file was huge there would be some space  
savings from having multiple sessions referencing the same PDB file.   
Nonetheless, the space issue is a lot less important for structure  
files than volume files.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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