setting pdb path for local mirror
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. -- Got No Time? Shop Online for Great Gift Ideas! http://mail.shopping.com/?linkin_id=8033174
Moo Cow writes:
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"
Python has a "special" way of writing indices: The subsequence is formed excluding the final index, so s[1:3] means the second and third character of s (indices 1 and 2), but excluding the fourth at index 3. -Christoph -- | Christoph Best <cbest@rzg.mpg.de> http://www.rzg.mpg.de/~cbest | Max-Planck-Institut fuer Biochemie, Munich, Germany +49-89-8578 2634
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.
-- Got No Time? Shop Online for Great Gift Ideas! http://mail.shopping.com/?linkin_id=8033174
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Christoph Best -
Eric Pettersen -
Moo Cow