[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
>>
>>
>>
>> _______________________________________________
>> cctbxbb mailing list
>> cctbxbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20130410/df2e945c/attachment.htm>
More information about the cctbxbb
mailing list