Hi Nat, On Apr 10, 2013, at 4:20 PM, Nathaniel Echols wrote:
The monomer library does indeed contain many files that don't conform to the official CIF standard, but that usually isn't a problem because the strict parsing is supposed to be disabled. Is the script you're running mmtbx/dynamics/tst_sa.py?
Yes, that is the script I'm running.
Try setting the environment variable LIBTBX_DISABLE_TRACEBACKLIMIT and re-run, and send us the traceback.
Here's the results: % setenv LIBTBX_DISABLE_TRACEBACKLIMIT 1 % cctbx.python ./tst_sa.py Traceback (most recent call last): File "./tst_sa.py", line 267, in <module> exercise_1() File "./tst_sa.py", line 122, in exercise_1 pi = get_pdb_inputs(pdb_str=pdb_str_1) File "./tst_sa.py", line 108, in get_pdb_inputs rama_potential=None, log = None) File "/usr/local/cctbx/cctbx_sources/mmtbx/command_line/real_space_refine.py", line 37, in get_processed_pdb_object mon_lib_srv = mmtbx.monomer_library.server.server() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 223, in __init__ list_cif = mon_lib_list_cif() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 63, in mon_lib_list_cif strict=strict) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 57, in __init__ self.cif = read_cif(file_name=self.path) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 92, in read_cif return iotbx.cif.reader(file_path=file_name, strict=False).model() File "/usr/local/cctbx/cctbx_sources/iotbx/cif/__init__.py", line 71, in __init__ raise CifParserError(self.parser.parser_errors()[0]) CifParserError: /Applications/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif(line 1) : error 4 : Unexpected token, at offset -1 near global : unexpected input... expected one of : Actually dude, we didn't seem to be expecting anything here, or at least I could not work out what I was expecting, like so many of us these days! James