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

_______________________________________________
cctbxbb mailing list
cctbxbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/cctbxbb