[Chimera-users] setting pdb path for local mirror

Eric Pettersen pett at cgl.ucsf.edu
Mon Dec 17 11:22:25 PST 2007

	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 Pettersen
                         UCSF Computer Graphics Lab

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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