[Chimera-users] PDB

Eric Pettersen pett at cgl.ucsf.edu
Wed Jun 23 13:51:00 PDT 2010

Perhaps the situation is that you have the same session using dozens  
or hundreds of copies of the same PDB file?


On Jun 23, 2010, at 1:47 PM, Eric Pettersen wrote:

> 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
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
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