Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: 2017 COMCIFS report

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@iucr.org> wrote:

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 :-)?


On 08/05/2018 06:06, James Hester wrote:

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.


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

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.

comcifs mailing list

comcifs mailing list

T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148

Reply to: [list | sender only]