[cctbxbb] cif parser & ccp4 mon_lib incompatibility

Nathaniel Echols nechols at lbl.gov
Wed Apr 10 15:38:04 PDT 2013


Actually, I think there may be a problem with your CCP4 installation - the
exact same file on my computer starts with "global_", while yours lacks the
trailing underscore, and editing mine to match reproduces the crash.  With
the underscore in place it should work (assuming nothing else has changed).


On Wed, Apr 10, 2013 at 3:28 PM, James Stroud <xtald00d at gmail.com> wrote:

> 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
>
>
>
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>
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