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

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 2 09:40:30 PST 2010

Hi Mark,
That is your fetch download directory, where to put files fetched over  
the Web.  It will also check there to avoid fetching things that have  
been previously fetched, and as you said, it is just a single PDB  
directory with everything in it.

However, (if I understand you correctly) what you are asking about is  
a hierarchical local installation, which is set as described in my  
previous message, by editing a file to contain the desired leading  
path.   So yes, you do need to do that.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 2, 2010, at 9:30 AM, Mark Moll wrote:

> Elaine,
> I have set the Fetch and PDB Preferences to look for pdb files in my  
> local installation in my home directory. Are you saying that this is  
> not sufficient, and that I still need to change the path in share/ 
> chimera/pdbDir?
> <Fetch.png><PDB.png>
> I must be missing something
> On Mar 2, 2010, at 11:17 AM, Elaine Meng wrote:
>> 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:
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html#local>
>> 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
>> -----
>> 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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