[cctbxbb] cif parser & ccp4 mon_lib incompatibility

Richard Gildea rgildea at gmail.com
Wed Apr 10 21:56:38 PDT 2013


The unquoted word 'global_' (with trailing underscore) is part of the STAR
file syntax (upon which CIF is based), but is explicitly forbidden in the
formal CIF syntax:

http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax#global

However, for compatibility with the monomer library which is using the
global_ keyword despite it being forbidden in the CIF syntax, we added
support for a non-strict mode of the CIF parser in the iotbx which could
support global_ data blocks. Of course, if the trailing underscore is lost,
then it is a syntax error either way, as the parser is looking for the
start of a data block, signified by a data block heading (starting with
'data_').

Cheers,

Richard


On 10 April 2013 16:24, Oleg Dolomanov <oleg at olexsys.org> wrote:

> Sorry, yes,'global_' is also a special global data block and should work...
>
> ------------------------------
> From: nechols at lbl.gov
> Date: Wed, 10 Apr 2013 16:17:53 -0700
>
> To: cctbxbb at phenix-online.org
> Subject: Re: [cctbxbb] cif parser & ccp4 mon_lib incompatibility
>
> On Wed, Apr 10, 2013 at 4:12 PM, Oleg Dolomanov <oleg at olexsys.org> wrote:
>
> 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.
>
>
> This would be true when using the CIF reader on its own, but for
> macromolecular apps (including the test script that's failing), we disable
> this error checking specifically for the CCP4 monomer library.  In fact the
> version we distribute with Phenix
> ($PHENIX/chem_data/mon_lib/list/mon_lib_list.cif) starts like this:
>
> global_
> _lib_name         mon_lib
> _lib_version      4.11
> _lib_update       15/04/05
>
> It is very likely that we may start to distribute the entire chem_data
> tree from our web site as an optional add-on, which will greatly ease the
> use of CCTBX in other macromolecular applications (e.g. MolProbity).  Of
> course the CCP4 version will be more complete and up-to-date, although a)
> some of those restraints are not especially well-validated, and b) we
> incorporate additional information in the restraints we distribute.
>
> -Nat
>
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