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(72) pdCIF dictionary approved; Review of COMCIFS
- To: COMCIFS@iucr.ac.uk
- Subject: (72) pdCIF dictionary approved; Review of COMCIFS
- From: bm
- Date: Wed, 9 Jul 1997 17:13:29 +0100
Dear Colleagues
A72.1 Approval of pdCIF draft dictionary
----------------------------------------
COMCIFS has unanimously endorsed the draft powder diffraction CIF dictionary,
version 0.996, as posted on 12 March 1997, subject to editorial corrections
and the incorporation of the revisions listed below. It should be noted that
Paula Fitzgerald still expresses reservations about the looseness of the
category assignments in the dictionary.
This may be taken as the formal adoption by the IUCr of pdCIF as the
preferred archive file format for powder diffraction data and structural
reports. The official release version will be made available to the
community upon completion of editorial and proofing stages; I shall discuss
with Brian a likely timescale for this process. Software developers may be
directed to the draft version 0.996 as a good indicator of the overall
structure and content of the final version, but should be warned of the
possibility of some change between this and the official published version.
I shall report on any editorial revisions and the manner of presentation of
the dictionary and its associated documentation as we work through the
'publication' process with Brian. Thanks, as always, go to all those who
have contributed to the work involved in this project.
***
The major addition to the draft version 0.996 will be the addition of the
following data definitions to permit the establishment of cross-linked
sub-tables in the PD_DATA category (constructive suggestions on the wording
of the definitions or choice of names are still welcome):
data_pd_data_[pd]
_name '_pd_data_[pd]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_pd_meas_intensity_total
_pd_proc_ls_weight
_pd_proc_intensity_bkg_calc
_pd_calc_intensity_total
240(15) 0.00417 214.5 214.5
219(15) 0.00457 214.3 214.2
206(14) 0.00485 214.0 214.0
212(15) 0.00472 213.8 213.7
190(14) 0.00526 213.5 213.5
203(14) 0.00493 213.2 213.2
# - - - - data truncated for brevity - - - -
;
; Example 1 - data set collected for a two-phase sample (Al~2~O~3~/Si)
by B. H. Toby, '1997-01-29T16:37|POWSET_01|B.Toby|..NIST-D5000'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_pd_meas_point_id
_pd_meas_intensity_total
1 240(15) 2 219(15) 3 206(14) 4 212(15) 5 190(14) 6 203(14)
loop_
_pd_proc_point_id
_pd_proc_ls_weight
_pd_proc_intensity_bkg_calc
1 0.00417 214.5 2 0.00457 214.3
3 0.00485 214.0 4 0.00472 213.8
5 0.00526 213.5 6 0.00493 213.2
loop_
_pd_calc_point_id
_pd_calc_intensity_total
1 214.5 2 214.2 3 214.0 4 213.7 5 213.5 6 213.2
;
; Example 2 - the data of Example 1 split into three separate tables.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_pd_meas_point_id
_pd_meas_2theta_scan
_pd_meas_intensity_total
1 21.0 24
2 21.2 32
3 21.4 67
4 21.6 98
loop_
_pd_calc_point_id
_pd_calc_2theta_scan
_pd_calc_intensity_total
1 21.0 26
1a 21.3 56
4 21.6 76
4a 21.9 90
;
; Example 3 - hypothetical example where the measured and calculated
points are not in one-to-one correspondence.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; The PD_DATA category contains raw, processed and calculated
data points in a diffraction dataset. In many cases, it is
convenient to tabulate calculated values against the
raw and processed measurements, and so the various
_pd_meas_, _pd_proc_ and _pd_calc_ data items belonging
to this category may be looped together. In some instances,
however, it makes more sense to maintain separate tables of
the data contributing to the measured and processed
diffractograms (for example a profile may be calculated
at two-theta values different from those of the measured
data points). To facilitate the identification of equivalent
points in these separate tables, separate identifiers are
defined.
;
data_pd_calc_point_id
_name '_pd_calc_point_id'
_category pd_data
_related_item '_pd_data_point_id'
_related_function alternate
_definition
; Arbitrary label identifying a calculated data point. Used to
identify a specific entry in a list of values forming the
calculated diffractogram. The role of this identifier may
be adopted by _pd_data_point_id if measured, processed and
calculated intensity values are combined in a single list.
;
data_pd_data_point_id
_name '_pd_data_point_id'
_category pd_data
_definition
; Arbitrary label identifying an entry in the table of
diffractogram intensity values.
;
data_pd_meas_point_id
_name '_pd_meas_point_id'
_category pd_data
_related_item '_pd_data_point_id'
_related_function alternate
_definition
; Arbitrary label identifying a measured data point. Used to
identify a specific entry in a list of measured intensities.
The role of this identifier may be adopted by
_pd_data_point_id if measured, processed and calculated
intensity values are combined in a single list.
;
data_pd_proc_point_id
_name '_pd_proc_point_id'
_category pd_data
loop_ _related_item
_related_function
'_pd_data_point_id' alternate
'_pd_meas_point_id' alternate
_definition
; Arbitrary label identifying a processed data point. Used to
identify a specific entry in a list of processed intensities.
The role of this identifier may be adopted by
_pd_data_point_id if measured, processed and calculated
intensity values are combined in a single list, or by
_pd_meas_point_id if measured and processed lists are
combined.
;
D70.1 Review of COMCIFS
-----------------------
I append a couple more contributions to the general call for a review, and
then David Brown's formal proposal for a modified structure for the
committee. David will be away from the start of the ACA meeting
(approximately 18 July) until the end of August, so he needs to know rather
quickly whether this can serve as the basis for a submission to the
Executive Committee, who meet in Lisbon during August.
Herbert Bernstein writes:
HB> I am certain Syd's ideas on the formal organization of COMCIFS are
HB> sound, but I would like to recommend an informal practice for your
HB> consideration -- creation of a COMCIFS list-server and web-based display
HB> of the message archive in the manner of the one set up by John Westbrook
HB> for mmCIF. This would give you Syd's non-voting consultants on a
HB> dynamic, volunteer basis with minimal fuss in a way that allows a newly
HB> interested party to review the state of the discussion easily. We are a
HB> remarkably civilized community and, at least in the mmCIF case, managed
HB> to discuss many challenging issues without the need for explicit
HB> moderation of each message. Most people had the very good sense to find
HB> a moderator (usually Paula) when they thought one was needed, and, as far
HB> as I know, John never had to throw anyone off the distribution list (an
HB> action which would have stopped them from sending messages as well).
This is certainly a useful suggestion, and I've been considering for some
time the setting up of a general discussion forum for software developers.
We have been looking at a web conferencing system (called HyperNews), but
there are some problems in managing something like this across web servers
on low-bandwidth lines; and on the other hand in making the contributions
visible across mirror sites without installing server-side software. So I am
certainly open to suggestions on the best mechanism for doing this sort of
thing (John's system is one contender). How to implement it may depend also
on the state into which COMCIFS evolves.
Howard Flack writes:
HF> I'm surprised by Syd's 'Wedding cake' model of a possible future
HF> structure for COMCIFS. From what I could understand from the discussion
HF> on the powder dictionary, it seemed to me that BT was being criticized
HF> for a lack of compatibility with other CIF developments because he had
HF> been working in a closed group.
HF>
HF> The success of CIF will only come from working applications being
HF> available to the general public.
I think I would dispute Howard's interpretation of the factors at work in
the pdCIF case, but I think there is a real danger of people working in
isolation and going astray. For that reason I support a future model in
which new working groups do have some association with existing COMCIFS
members, who will perhaps act as their 'guardian angels' and keep them from
getting lost. There is also a need for better documentation of the decisions
reached by COMCIFS down the ages, and I'll try to attend to that on the IUCr
web site, now that we at last have the first raft of new dictionaries
approved. Also, I think there should be continued sponsorship of workshops
and other events where people will get a chance to discuss CIF matters face
to face. While doing everything by e-mail is possible, it's not always the
fastest or most efficient way of achieving things.
David's proposal now follows:
PROPOSALS FOR A NEW STRUCTURE FOR COMCIFS
I.D.Brown
This proposal is based on suggestions received to 1997.7.8
I. THE PURPOSE OF COMCIFS
1. To establish policies defining the use of the Crystallographic
Information File (cif).
2. To receive and examine all proposed amendments and extensions to
the cif standard. In particular, to ratify proposed data names,
ensure that the data structures conform to the basic cif
specifications, and to ensure that the defintions of data items are
clear and unambiguous.
3. To ensure that all accepted amendments and extensions to the cif
standard are announced in an approporiate publication or news item
in an IUCr publication.
4. To ensure that adequate current documentation of the cif
standard is available to potential users in both printed and
machine-readable forms.
5. To coordinate with other organisations proposing cif related
dictionaries using STAR files to ensure maximum compatibility
between cifs and related file structures.
6. To coordinate with other crystallographic organisations
proposing non-cif standards to ensure maximum compatibility.
7. To coordinate with writers of software intended to read and
write cifs.
II. MEMBERSHIP OF COMCIFS
1. Voting members
COMCIFS should consist of 6 voting members appointed by the
Executive Committee of the IUCr on the recommendation of Comcifs.
Membership would normally be for a three year renewable term. A
membership slate will be presented to the Executive Committee of
the IUCr for approval following each IUCr Congress. Voting members
will be knowledgeable in the area of electronic manipulation of
information and representative of the various fields of
crystallography.
Comcifs will have a chair and secretary appointed by the Executive
Committee. The secretary need not be a voting member.
2. Organisational Representatives
Comcifs membership will include organisational representatives who
will receive all Comcif mailings and who are free to comment on any
Comcifs business particularly that related to the work of their
organisation. Organisational representatives will have no vote.
Organisational representatives are appointed by organisations, such
as data centers and commissions of the Union, to represent their
interest. Organisations authorised to appoint representatives
must be approved by Comcifs. There is no limit to the number of
organisations that may appoint representatives.
3. Observers
Observers are individuals wishing to participate in, or be aware
of, Comcifs business. They will receive all Comcifs mailings are
are free to comment on any Comcifs business. Observers will have
no vote.
Observers are appointed at the discretion of the chair of Comcifs.
There is no limit to the number of observers that may be appointed.
III. ORGANISATION OF COMCIFS
1. Mode of operation
The business of Comcifs will be normally carried out by email.
2. Working Parties
Comcifs will establish working parties, possibly in conjunction
with other organisations, to prepare or maintain dictionaries or
software, or to engage in any other project appropriate to Comcifs'
objectives. The working parties may consist of any number of
members but will include representatives of interested
organisations and those knowledgeable in the area. It is not
necessary that a voting member of Comcifs be a member of the
working party.
3. Subcommittees
For each working party, Comcifs will establish a subcommittee to
oversee Comcifs interest in the project. Subcommittees will be
appointed by the chair of Comcifs. Each subcommittee will consist
of at least one voting member of Comcifs and the chair of the
working party or delegate. The purposes of the subcommittee are:
a. To advise the working party on cif standards.
b. To act as liaison between Comcifs and the working party,
bringing to Comcifs for discussion and resolution any matters that
might require changes or clarifications in cif policy.
c. To ensure that items such as dictionaries presented to Comcifs
for approval conform to cif standards.
---------------------
Regards
Brian
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