[cctbxbb] cif parser & ccp4 mon_lib incompatibility

James Stroud xtald00d at gmail.com
Wed Apr 10 15:28:10 PDT 2013

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:

% cctbx.python ./tst_sa.py
Traceback (most recent call last):
  File "./tst_sa.py", line 267, in <module>
  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
  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!


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