2017 COMCIFS report

James Hester jamesrhester at gmail.com
Tue May 8 14:40:32 BST 2018

Another idea is might be to run a monthly low-tech ASCII newsletter for
distribution on the mailing lists, with things like summaries of
discussions on Github or other mailing lists, short articles on particular
aspects of the new standards, user profiles, CIF programming tips, maybe a
series of short articles on writing dictionaries, Q and A, opinion pieces
etc. (not all of these every time, necessarily). Unfortunately it would
need a reasonably dedicated editor to get it started and I'm not sure there
is anybody with the time right now.

On 8 May 2018 at 19:13, Brian McMahon <bm at iucr.org> wrote:

> James
> I'm happy with this report in its current form.
> The "looking forward" comment is very sensible. How about a small
> competition with cash prize to write a specific piece of
> open-source software (python/perl bindings to CIFAPI,
> CIF2-compatible update to Perl STAR::Parser, checkCIF module for
> magCIF :-)?
> Brian
> On 08/05/2018 06:06, James Hester wrote:
>> Dear COMCIFS,
>> A draft report for COMCIFS for the 2017 calendar year is appended below
>> for your comment and approval. This must be submitted to the IUCr by the
>> end of the week.
>> James.
>> --
>> COMCIFS report 2017
>> ===================
>> COMCIFS is responsible for maintaining and developing the suite of
>> standards known as the Crystallographic Information Framework (CIF) on
>> behalf of the IUCr. The committee consists of five voting members and
>> a broad collection of advisers and observers. The current voting
>> members are James Hester (Chair), Brian McMahon (Secretary), Herbert
>> Bernstein, John Westbrook, and John Bollinger. No issues required a
>> vote in 2017.
>> New dictionaries
>> No new dictionaries were approved in 2017. Preliminary drafts of a
>> high pressure dictionary and a topological dictionary were sighted.
>> Updating legacy dictionaries
>> COMCIFS is in the process of rewriting all legacy IUCr dictionaries to
>> use a modern dictionary definition language (DDLm).  This work is now
>> essentially complete for core, powder, twinning and
>> constraint/restraint dictionaries. The modulated structure dictionary
>> required development of further standards in order to properly
>> describe data spread over multiple blocks; a recommendation was
>> developed and formally proposed at the end of the year.
>> The legacy dictionaries are being gradually phased out, with a
>> maintainer appointed to ensure that the legacy dictionaries remain
>> compatible with the new dictionaries in the overlap period.
>> Macromolecular standards
>> The wwPDB is responsible for a large and rapidly expanding collection
>> of CIF definitions that encompass concepts and techniques used in the
>> macromolecular community. The wwPDB continues to develop powerful
>> tools for easy deposition of, and access to, data in mmCIF/PDBx form,
>> and continues to encourage an active community of users. In 2017, the
>> wwPDB PDBx/mmCIF Working Group has drafted extensions describing
>> macromolecular coherent diffraction experiments including definitions
>> for describing data collection on potentially vast numbers of crystal
>> samples.
>> Interactions with other standards groups
>> Collaboration with the NeXus project on harmonising standards took a
>> major leap forward during the Hyderabad meeting, with the approval by
>> NeXus representatives of a method for wholesale incorporation of CIF
>> data into NeXus files. This is initially intended as a way for NeXus
>> users to include experimental and sample information defined in
>> mmCIF/PDBx dictionaries into raw data files, and is sufficiently
>> flexible to allow any data names defined in CIF dictionaries to be
>> included in a NeXus file. With the increasing adoption of Dectris
>> Eiger Dectectors at macromolecular crystallogrpaphic synchrotron
>> beamlines, it has become routine practice to use automatic software
>> translation from the Eiger HDF5/Nexus data format to the imgCIF/CBF
>> format both on-the-fly and via file systems.
>> COMCIFS is also closely involved with the new IUCr Committee on Data
>> (CommDat). Chairs of both committees attended the committee meetings
>> for COMCIFS and inaugural meeting for CommDat held during the
>> Hyderabad congress.
>> A standard for writing CIF data in the JSON format was approved
>> by COMCIFS during 2017. It is expected that this will be useful when
>> transferring structural data within web-based applications.
>> Hyderabad meeting
>> COMCIFS sponsored a one-day workshop devoted to creating CIF
>> dictionaries prior to the IUCr Hyderabad congress, with about 15
>> registered attendees.  There was also a well-attended microsymposium
>> discussing programming for CIF, NeXus and related file structures
>> (MS107). A COMCIFS committee meeting was also held during the congress.
>> Looking forward
>> Over the last few years a considerable amount of work has fallen to a
>> handful of people. This situation is not sustainable, particularly as
>> the first generation of CIF experts move into retirement. The chair
>> plans to explore strategies to expand the community of people actively
>> engaged with CIF development.
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