[cctbxbb] cif parser & ccp4 mon_lib incompatibility

Wed Apr 10 16:12:37 PDT 2013

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: xtald00d at gmail.com
Date: Wed, 10 Apr 2013 16:58:40 -0600
To: cctbxbb at phenix-online.org
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 <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.pyTraceback (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 leastI could not work out what I was expecting, like so many of us these days!

James

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