[cctbxbb] cif parser & ccp4 mon_lib incompatibility

[James Stroud]

Hi Nat,

On Apr 10, 2013, at 4:44 PM, Nathaniel Echols wrote:
> 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?

Thanks for tracking this down. The installer I used was double-clickable black-box "foolproof" no-thinking point-and-click: ccp4-6.3.0.2-arp.dmg

I just ran the updater (bin/update) but it didn't touch mon_lib_list.cif even though it reported to complete successfully. If I have more cif problems, I'll download the latest ccp4 sources and see what happens when I build from scratch.

James



> 
> 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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