I should add about cif is that there exists a number fundamental
incompatibilities between pdCIF & mmCIF. One main issue, as I understand
it, is that pdCIF naturally can describe multiple data sets (powder
patterns) used in a single structure analysis - mmCIF seems to forbid
this. This will cause trouble with the advent of multiple powder
patterns used in protein structure analyses. Atom naming conventions are
also different. The cif "factotum" committee must address this while
moving to new descriptions for cif (DDL3??).
R.B. Von Dreele
IPNS Division
Argonne National Laboratory
Argonne, IL 60439-4814
-----Original Message-----
From: Brian H. Toby [mailto:[EMAIL PROTECTED]
Sent: Thursday, February 22, 2007 9:44 AM
To: rietveld_l@ill.fr
Subject: Powder Diffraction In Q-Space: plotting CIFs
On Feb 22, 2007, at 4:54 AM, Alan Hewat wrote:
Now this sounds interesting. Certainly the raw data
should be archived and people could then plot it as they wish. But are
there examples of interactive plotting applications embedded in
powderCIF files, and what language might they use ? I would like to see
a profile plotting package in Java or some other really portable
language that would read in CIF files and plot calculated-observed
patterns like Jmol now plots structures.
Alan.
A large part of my motivation for the decade I invested in pdCIF
was that postage stamp size plots do not allow one to really understand
the quality of a Rietveld analysis fit. The pdCIFplot application will
plot in Q, provided the software has the information needed to convert
the supplied units (it does not know how to convert energy or
time-of-flight, but does fine with 2theta or d-space). It can be used to
plot intensity/s.u. -- although that is a rather clumsy thing to set up
in the "custom plot" menu. The source code (Tcl/Tk) is distributed, so
if anyone would like to add new features -- I'd love to get them. I
should also plug my work by noting that pdCIFplot also allows plotting
of Bill David's reduced chi squared or (obs-calc)/sigma and will show
the relationship between the intensity scale will also allow one to look
at the relationship between the reported intensity scale and the
equivalent value as "counts". (See www.ncnr.nist.gov/xtal or CCP14 for
ciftools downloads; N.B. the pdCIFplot paper is open access:
http://journals.iucr.org/j/issues/2003/05/00/aj0008/aj0008.pdf)
pdCIFplot is not an application embedded in a user's CIF (in
fact DDL3 embeds apps in the dictionary not in the files), nor is it
embedded in a web browser -- though I think that could be possible.
Alan, perhaps you might be able to figure out how to configure firefox
to launch pdCIFplot when it encounters a .CIF file on various platforms?
There is an open question of how pdCIF will get updated from
DDL1 to DDL3. The pdDMG needs a new chair willing to take pdCIF into the
next decade. I think I have paid my dues. I will not make any (more?)
enemies by suggesting suitable candidates.
Brian
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Brian H. Toby, Ph.D. office:
630-252-5488
Materials Characterization Group Leader, Advanced Photon Source
9700 S. Cass Ave, Bldg. 433/D003 work cell:
630-327-8426
Argonne National Laboratory secretary (Marija):
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Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot
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