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Hi Mark<br>
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I've improved Chimera personal PDB directories (set with Preferences
/ PDB) so that if the PDB file is not found assuming a flat-file layout
then in looks for the file in those directories assuming a hierarchical
layout, e.g. personal-dir/fa/pdb1fav.ent. This will be in tomorrow's
Chimera daily builds. Formerly you had to edit Chimera code (file
chimera/share/chimera/pdbDir) in order to add a PDB directory where the
files are in a hierarchical layout.<br>
<br>
Tom<br>
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<blockquote cite="mid:EC6BFE3A-3D6D-4EE6-A285-CF664EF21E2E@cs.rice.edu"
type="cite">
<pre wrap="">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?
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I must be missing something
On Mar 2, 2010, at 11:17 AM, Elaine Meng wrote:
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<pre wrap="">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:
<a class="moz-txt-link-rfc2396E" href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html#local"><http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html#local></a>
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:
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<pre wrap="">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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