[Chimera-users] load pdb files from local PDB mirror

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 2 09:17:25 PST 2010

Hi Mark,
Chimera does expect the hierarchical arrangement for a local  
installation, but you may need to edit what is used for the leading  
part of the path.  The defaults are /mol/pdb/ and /usr/mol/pdb/  
whereas it sounds like you will need to change that to include your  
home directory, as described here:


Chimera resorts to web fetch when it does not find the local  
installation, so once you fix the local installation path, it will not  
need to do that.  If there is no local installation, depending on your  
preferences it may next check the download directory to see if you've  
already fetched the file, and if not then get the file over the web  
from the PDB.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 2, 2010, at 9:05 AM, Mark Moll wrote:

> I have a local mirror of all PDB structures (as pdb files). It’d be  
> nice if Chimera could use this, but it seems that Chimera expects a  
> “flat” directory structure rather than the hierarchical directory  
> structure of the PDB. For example, on my machine the pdb file for  
> 1ady is stored in ${HOME}/pdb/ad/pdb1ady.ent.gz, but when I fetch by  
> ID, the file will not be found. Instead, Chimera will download the  
> file and save it in ${HOME}/pdb/PDB/1ADY.pdb.
> Is there some way to handle both cases (flat & hierarchical  
> directory structure)?
> -- 
> Mark
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> Chimera-users at cgl.ucsf.edu
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