[cctbxbb] cif parser & ccp4 mon_lib incompatibility

Nathaniel Echols nechols at lbl.gov
Wed Apr 10 15:44:09 PDT 2013


PS.  Actually, there are other differences:

global_
_lib_name      mon_lib
_lib_version   5.39
_lib_update    06/11/12

So it's three months newer than the one you're using.  Have you run the
CCP4 updater?


On Wed, Apr 10, 2013 at 3:38 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> 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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>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>
>>
>
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