Hi,

the CIF parser will report this error if any of the CIF items is outside data_ or save_ blocks. So you need to change 'global' to 'data_global' to prevent this error.

Cheers,

o

From: [email protected]
Date: Wed, 10 Apr 2013 16:58:40 -0600
To: [email protected]
Subject: Re: [cctbxbb] cif parser & ccp4 mon_lib incompatibility

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 <[email protected]> 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 <[email protected]> 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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