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(81) Call for votes on revised terms of reference; coreDMG list

  • To: COMCIFS@iucr
  • Subject: (81) Call for votes on revised terms of reference; coreDMG list
Dear Colleagues

This circular falls into three sections. In section A I call for votes to
approve the proposed revised terms of reference for COMCIFS. In Section B
I describe the new structure that has been established for the maintenance
of the Core Dictionary. In Section C I group together the remaining items of
discussion that I received since last time. These all relate to the
maintenance of the Core, and thus fall into the domain of the coreDMG
discussions; I include them here solely for the record and to provide a
bridge into the coreDMG discussions for members who wish to proceed further
with these topics. There will be no further discussion of these items within
this series of circulars.

Correspondent are identified as: D> David Brown, H> Howard Flack, G> George
Sheldrick.

A. Call for votes on proposed new terms of reference
====================================================

D79.1 COMCIFS report
--------------------
D> 	I agree with Howard's first two (minor) suggestions and will
D> incorporate them into the report.
D> 
D> 	In response to his third suggestions, I propose to add a second
D> clause to the first of the purposes of COMCIFS so that it now reads:
D> 
D> '1. To establish policies defining the use of the Crystallographic
D> Information File including which STAR features and which Dictionary
D> Definition Languages (DDL) should be used.'

*** All FULL MEMBERS of COMCIFS are requested to vote aye or nay on acceptance
*** of the revised terms of reference for the Committee as listed in circular
*** 79 and amended according to the above paragraph.


B. CoreDMG Discussion List
==========================

In accordance with the revised working practices that we have discussed in
establishing the new terms of reference, a mailing list has been set up
for technical discussions on the maintenance of the Core dictionary. The
list will be used by the Core Dictionary Maintenance Group, whose initial
membership by invitation of the Chairman of COMCIFS is
     I.D. Brown (Chair)
     S.R. Hall
     P.R. Edgington
     A.L. Spek
     B. McMahon
  Consultant:  J. Westbrook

Membership of the mailing list is formally restricted to members of and
consultants to this group, but any member of COMCIFS may apply to be added
to the list by sending to the address listproc@iucr.org an email message
containing the line
   subscribe coredmg <Your Name>

Please note that if you wish to be involved in further discussions on any of
the remaining topics in this circular, you will need to follow the above
procedure. Once your subscription has been processed, communications to the
list itself (i.e. contributions to the coreDMG discussions) should be sent
to the address coredmg@iucr.org.

All coreDMG discussions will be posted for public reading at the URL
http://www.iucr.org/iucr-top/lists/coredmg/ (or via the CIF home page),
and members of COMCIFS who choose not to subscribe to the coreDMG list may
always read this archive and post occasional comments through me.


C. coreDMG issues for discussion
================================
(Note: these topics have all been entered into a seed archive for the
coreDMG discussion list. Members may find it convenient to respond
by reading the discussion on the WWW page and using the relevant hot links.)

D77.2 Absolute structure
------------------------
H>D> 	Howard and I seem to have quite different ideas about what is
H>D> expected in the _reflns_number_* fields.  
H> 
H>   This just proves that they are ill-defined. 

H>D> 	I like Howard's definitions of _chemical_absolute_configuration
H>D> and _chemical_optical_rotation, and we should also consider renaming the
H>D> items _refine_ls_abs_structure_* to _refine_ls_absolute_configuration_*
H>D> with Howard's enhanced definition. 
H> 
H>  I disagree entirely. The least-squares refined Flack x parameter applies to
H> absolute structure which is a much wider concept than absolute
H> configuration. The current name is fine and should be left as it is.
H> Absolute structure occurs in all non-centrosymmetric structures, absolute
H> configuration in only a subset. To interpret absolute configuration needs
H> the absolute structure parameter value (or something equivalent) and other
H> conditions defined in _chemical_absolute_configuration.

D> 	Howard points out the importance of relating the absolute
D> configuration of a molecule to its optical rotation in a crystal.  This is
D> fine for molecular crystals, but quite often authors report the absolute
D> configuration of an inorganic crystal that dissolves to form an optically
D> inactive solution (if it dissolves at all).  I find that in such papers
D> the authors proudly present the Flack parameter as evidence of having
D> determined the absolute configuration, but generally fail to relate this
D> to any other physical property!  For such compounds it is largely a matter
D> of luck which enantiomer the authors have selected because one would
D> expect equal numbers of right and left handed crystals to appear in any
D> preparation.  I would therefore like to add to Howard's definition,
D> presumably at the end of the first paragraph, the following: 
D> 
D> 	'For non-molecular crystals it is recommended that the absolute
D> configuration determined by diffraction methods be related to some other
D> physical property, such as morphology, that can be used to distinguish
D> between crystals of opposite chirality.'

D80.3 Extent of measured data
-----------------------------
D> 	I agree with George that we should replace *_theta_max_* with
D> *_resolution_* wherever possible, and certainly in any new items we
D> define.  We must be careful, however, not to get names confused with
D> _diffrn_detector_area_resolution_mean which refers to quite a different
D> type of resolution.  What about: 
D>  
D> 	_diffrn_reflns_measured_fraction_resolution_full
D> 	_diffrn_reflns_measured_fraction_resolution_max
D> 	_diffrn_reflns_resolution_full
D> 	_diffrn_reflns_resolution_max (alternative to *_theta_max)
D> 
D> All of these should belong to the category diffrn_reflns, not the
D> categories shown in circular 76.

H>G>I would also like to repeat a further suggestion
H>G> that I made in D71.1 (discussing the Acta 97 instructions for authors)
H>G> that it is illogical to define: 
H>G> 
H>G> data_diffrn_measured_fraction_theta_full
H>G> data_diffrn_measured_fraction_theta_max
H>G> 
H>G> and
H>G> 
H>G> data_diffrn_reflns_theta_full
H>G> 
H>G> using the Bragg angle 'theta' rather than the resolution in Angstroms
H>G> (which is how a protein crystallographer would have defined it). 
H>G> Whereas the resolution gives an immediate indication of the extent of
H>G> the data (and hence the data to parameter ratio), theta depends on the
H>G> wavelength, which with increasing use of synchrotron data may be
H>G> different for different experiments.  Indeed for Laue data the
H>G> wavelength is different for each reflection and so 'theta' is useless
H>G> whereas 'resolution' would still be sensible.
H> 
H>   I agree entirely with George on this point. 
H>   The wavelength still needs to be indicated where monochromatic 
H>   radiation is used.  

H>G> Will COMCIFS be allowed to preview the 1998 Acta Cryst. instructions for
H>G> authors ?!  It might help to prevent accidents.
H> 
H>   I agree with George. It is not really the 'Notes for Authors' in their
H> entirety which is a matter for COMCIFS but rather the principle that any
H> official IUCr publication of new or modified CIF data names should contain
H> only those which have been discussed or approved within COMCIFS.

Regards
Brian