Hi,
The file "pdbDir" in the same directory as __init__.py defines what directory to look in for a PDB mirror distribution.  If you change the contents of that file to:

pdbDir = " /blah/blah/pdb/data/structures/divided/pdb"

then Chimera will find your mirror distribution.  The trouble is that if you install a new version of Chimera then that file will be overwritten.  So I've just committed a change to Chimera so that if you have a file named "pdbDir" in ~/.chimera/chimera then that file will be used instead of the one inside the Chimera distribution.  So if you get tomorrow's daily build it will have that change in it.
The "system PDB mirror finding" needs to be improved somehow so that a system administrator can specify where the mirror is and not have to have individual users place files in their home directories to specify it.

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu

On Dec 17, 2007, at 5:12 AM, Moo Cow wrote:

Sorry for an easy question.
Chimera has a hook to use a local mirror of the PDB (preferences-PDB)
I am too thick to see what path to give it. If you have the PDB,
you have the top level
   /blah/blah/pdb
the structure directory
   /blah/blah/pdb/data/structures/all
and the divided directory
   /blah/blah/pdb/data/structures/divided/pdb

When a non-python reader looks at the code (__init__.py), it
seems to be trying out the divided directory

    IDcode = IDcode.lower()
    subpath = IDcode[1:3] + os.sep + "pdb" + IDcode + ".ent"
    pdbDir = systemPDBdir()
    if pdbDir is not None:
             .....
but this does not look correct. The PDB divided path would want
    subpath  IDcode[1:2]
to get the subdirectory "pt" from a file like "5pti"

Many thanks and sorry for a seemingly daft question.


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