[cctbxbb] cif parser & ccp4 mon_lib incompatibility

Nathaniel Echols nechols at lbl.gov
Wed Apr 10 15:20:07 PDT 2013

On Wed, Apr 10, 2013 at 3:05 PM, James Stroud <xtald00d at gmail.com> wrote:

> =% cctbx.python ./tst_sa.py
> 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!
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?  Try setting the environment
variable LIBTBX_DISABLE_TRACEBACKLIMIT and re-run, and send us the

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