Hi,

I just received issue 46 of Scientific Computing World.
There is an article page 7 entitled "Materials Science Consortium
Grows" about MSI organizing membership around the
development of softwares. PowderSolve is mentioned
as one success of the 1998 and 1999 meetings. Members have the
exclusive right to use the software three years before it is released
to the general market.

Since there are some MSI staff members who have subscribed
to this Mailing List, I have one questions.

What is the annual fee for joining these Consortia ?

Best,


Armel Le Bail - Universite du Maine, Laboratoire des Fluorures,
CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France
http://www.cristal.org/


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Dear All,

There are now 124 subscribers to this mailing list.

On the What's New page of Endeavour, one can read  :

>April 28, 1999: Obviously ENDEAVOUR's concept is more and
>more accepted, since recently a nice 'clone' named 'ESPOIR'
>appeared, which has a striking similarity to ENDEAVOUR.
>However, you should check it out and compare them by yourself.

  http://www.crystalimpact.com/endeavour/about.htm

I disagree with 'clone' though I accept 'nice'. In order to obtain
a clone, which is in principle exactly identical to the parent from
which is extracted the DNA, you need to have access to a
mother cell. The Endeavour code is not open, so that It cannot
be cloned.

In fact, ESPOIR is a mutation of RMCA, a code for modelling
amorphous materials (R.L. McGreevy et al.) by Monte Carlo
with criteria of atom move acceptation based on the fit on
diffraction patterns+EXAFS+(...), and on shortest interatomic
distances and coordination constraints, with other nice features
(including an open code). Anyway, the volume of the original RMCA
code remaining in ESPOIR is less than 10%, because all the stuff
necessary for working around |F(hkl)|s was included (this part taken
from the ARIT Rietveld software). Finally, one can say that ESPOIR
results of the wedding of RMCA and ARIT. I recognize that the
ESPOIR birth motivation was the appearing of Endeavour, a nth
closed code of a quite long series of closed code (that are even
frequently unavailable as executable codes, I will not give names) in
the SDPD topic. Restoring the old academic concept of open codes
was my priority.

To what point ENDEAVOUR is not a mutation of RMCA, I don't
know.

I still wait for the solution of the SDPD Round Robin sample I
structure by ENDEAVOUR.

And I propose a challenge to the ENDEAVOUR team :
I use their samples (those with hkl given) and try to solve them
with ESPOIR. In the meantime, they use the ESPOIR samples
(CuVO3, PbSO4, TeI, [Co(NH3)5CO3]NO3.H2O, and cimetidine)
and try to solve them.

Is that not fair play ?

Best,


Armel Le Bail - Université du Maine, Laboratoire des Fluorures,
CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France
http://www.cristal.org/


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Andrzej Grzechnik wrote:

>I used ENDEAVOUR for some structures that I already knew to see how it works
>and whether it finds the structure. It actually does the thing. Then I used
>it for some unknown cases for which I had the total number of atoms in the
>unit cell, lattice parameters, and bad data (peak positions + intensities).
>No indexing. No structure factors. The most "complicated" case was with 20
>atoms, tetragonal lattice parameters, and 46 reflexions. I got a  structure
>(four independent atoms) that I refined with GSAS.

I had not seen that ENDEAVOUR could work from only peak positions +
intensities + composition, no indexing, no structure factor ?? I thought that
this was the domain of structure prediction by packing considerations,
knowing the molecular formula, for instance.

But for the tetragonal most "complicated" case, you had the cell, right ?
Then I guess that the 20 atoms correspond to a description in P 1 space
group ? In fact this is a 4 independent atoms structure, so that 46 reflections
appear sufficient for a refinement with GSAS. With ESPOIR, you may
expect to solve problems as complex as 15-30 independent atoms : 4 times
more complex. Of course, you will need approximately 10 time more
reflections than atoms (150-300 reflections). And they should be very good
data... They may be obtained by structure factor extraction methods (Pawley
and so on), provided you select those reflections not too much biased
by overlapping.

In fact, the next ESPOIR version, which is already working on my
desktop computer, will be able to use the whole set of extracted
reflections, whatever they are overlapping or not. This is not a miracle.
The test for accepting or rejecting an event in the Reverse Monte
Carlo process will not be made on the "|Fobs|", but on a pseudo
powder pattern reconstituted from those extracted "|Fobs|". You
may say, why not using the true powder pattern ? For saving
time, which is the main problem of Monte Carlo... By using this
pseudo pattern, you will not have to take account of background,
assymetry, Lorentz polarization, zeropoint, multiplicity (...).
Compared to methods of molecules location based on simulated
annealing (...), the number of DoF - Degrees of Freedom -
attains 45 to 90 in ESPOIR, against less than 20 (positions +
torsion angles) in, for instance, the school cases treated by the
Powder Solve software.

>Anyways, the idea of not using any potentials is a good one, providing that
>the minimum distances between atoms can be changed depending on the
>conditions of data collection. In my calculations for high pressure
>structures, I usually set them up to values 10% to 20% lower than the ones
>observed at ambient conditions.

In Espoir, the minimum distances and constraint coordinations
used in the version 0.9 were removed in version 1... All
appeared as if using minimum distances or not using them gave
the same result, with a very slight advantage to not using them !

I do not see why Endeavour could not succeed in problems
as complex as those solved by Espoir, since the Espoir code
is under GNU license (which does not exclude commercial
aspects, but force to let the source code open - but here may
be the problem ;-).

Coming back on Earth, you should realize that the number
of cases is small where Espoir or Endeavour will have a real
advantage on the classical direct or Patterson methods. These
are the last chance methods, to try when everything else failed.
So that they also will have large chances to fail in those
specially difficult cases...

Best


Armel Le Bail - Universite du Maine, Laboratoire des Fluorures,
CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France
http://www.cristal.org/


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At 01:32 10.05.99 +0200, Armel Le Bail wrote:
>Andrzej Grzechnik wrote:
>>In the description of the work by Armel Le Bail (ESPOIR), I can not find
anything
>>about potentials. What are they? My general comment about the Monte Carlo
>>approach is that it is very sensitive to the potential employed and, at
>>least, at the moment is not surpassing the direct methods in dealing with
>>low dimensional structures (not to mention the time of computing).
>
>No potential at all in ESPOIR. The program is intended to "surpass"
>direct methods in cases where the direct methods fail : bad powder
>data with strong overlapping, leading to few well estimated
>structure factors. The SDPD Round Robin sample II is somewhat
>exemplary on that point. Hard to solve with direct method (no
>participant of the Round Robin proposed a solution). Anyway, a
>solution is obtained from ESPOIR (with time, however INTEL
>announces already 3GHz for 2003, 64 bits ;-), although I did
>not succeeded with Endeavour. Endeavour may also be used
>without potential by considering lowest approach distances.
>
>What are the complexity of the structures that you were able
>to solve with Endeavour (number of independent atoms, space
>groups, number of reflections) ?
>
>Best,
>
>Armel Le Bail - Université du Maine, Laboratoire des Fluorures,
>CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France
>http://www.cristal.org/
>
>


Hi,

the structures that I'm dealing with and using Monte Carlo for are not as
complicated as the SDPD Round Robin sample II. These are the structures from
high pressure experiments. Usually at high P conditions, it is difficult to
entirely eliminate deviatoric stresses and preferred orientation effects.
For this reason, direct methods are not always successful, although EXPO is
able to estimate preferred orientation at the stage of intensity extraction.
Anyways, with such data, in most cases collected to 2 theta 25-30(lambda:
0.44-0.45), indexing and finding a space group is not a trivial matter. I
used ENDEAVOUR for some structures that I already knew to see how it works
and whether it finds the structure. It actually does the thing. Then I used
it for some unknown cases for which I had the total number of atoms in the
unit cell, lattice parameters, and bad data (peak positions + intensities).
No indexing. No structure factors. The most "complicated" case was with 20
atoms, tetragonal lattice parameters, and 46 reflexions. I got a  structure
(four independent atoms) that I refined with GSAS.

Anyways, the idea of not using any potentials is a good one, providing that
the minimum distances between atoms can be changed depending on the
conditions of data collection. In my calculations for high pressure
structures, I usually set them up to values 10% to 20% lower than the ones
observed at ambient conditions.

Regards,

Andrzej Grzechnik


----------------------------------------------------
  Andrzej Grzechnik
  Max-Planck-Institut fuer Festkoerperforschung
  Heisenbergstr. 1,  D-70569 Stuttgart,  Germany
  Tel: (++49) 711 689 1404;  Fax: (++49) 711 689 1444
  E-mail:  andrzej@...
----------------------------------------------------


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Andrzej Grzechnik wrote:
>In the description of the work by Armel Le Bail (ESPOIR), I can not find
anything
>about potentials. What are they? My general comment about the Monte Carlo
>approach is that it is very sensitive to the potential employed and, at
>least, at the moment is not surpassing the direct methods in dealing with
>low dimensional structures (not to mention the time of computing).

No potential at all in ESPOIR. The program is intended to "surpass"
direct methods in cases where the direct methods fail : bad powder
data with strong overlapping, leading to few well estimated
structure factors. The SDPD Round Robin sample II is somewhat
exemplary on that point. Hard to solve with direct method (no
participant of the Round Robin proposed a solution). Anyway, a
solution is obtained from ESPOIR (with time, however INTEL
announces already 3GHz for 2003, 64 bits ;-), although I did
not succeeded with Endeavour. Endeavour may also be used
without potential by considering lowest approach distances.

What are the complexity of the structures that you were able
to solve with Endeavour (number of independent atoms, space
groups, number of reflections) ?

Best,

Armel Le Bail - Université du Maine, Laboratoire des Fluorures,
CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France
http://www.cristal.org/


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Hi,

I'm just using ENDEAVOUR software that is based on reverse Monte Carlo. It
utilizes three types of potentials: Buckingham, Lennard-Jones, and simple
repulsion. I successfully used it to solve some structures of
three-dimensional solids. However, I have not had much success with two- or
one-dimensional structures. The potentials in ENDEAVOUR are simple and seem
to work well for the 3D cases. However, how can they account for Van der
Waals interactions between slabs or layers, for that instance? In the
description of the work by Armel Le Bail (ESPOIR), I can not find anything
about potentials. What are they? My general comment about the Monte Carlo
approach is that it is very sensitive to the potential employed and, at
least, at the moment is not surpassing the direct methods in dealing with
low dimensional structures (not to mention the time of computing).

Sincerely,

Andrzej Grzechnik


----------------------------------------------------
  Andrzej Grzechnik
  Max-Planck-Institut fuer Festkoerperforschung
  Heisenbergstr. 1,  D-70569 Stuttgart,  Germany
  Tel: (++49) 711 689 1404;  Fax: (++49) 711 689 1444
  E-mail:  andrzej@...
----------------------------------------------------


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Lachlan wrote :

>If this is a new robust method for powder indexing, it
>would be a shame to see it just gathering dust in the
>printed literture.   One perceived problem with new algorithms
>for structure solution from powder diffraction data is that
>many of them don't seem to make it beyond the printed word.

That problem would be overcome if some recommendations
to authors were added by J. Appl. Cryst. and others. Something
like : "Submission of papers dealing with new methods and
softwares will be returned if they are not accompanied with either
a public domain or commercial executable (or the source code)
allowing at least the reviewer to build a serious opinion on the
work."

Do you realize how many new methods and softwares were
only used by their authors, because of this lack of seriousness
of the IUCr journals (and others) ? At least, the structure factors
are sent in a CIF file, just in case the reviewer has any doubt
on some point.

Anyway, the J. Synchrotron Rad. paper (6, 1999, 67-92) reports
about only 2 tests :
          tetragonal Sr with a=5.653 A and c=3.043 A
and orthorhombic GaAs with a=4.968, b=4.773 and c=5.285 A.
Those examples are not what one could design as very
complicated, even if an impurity was present. If genetic
algorithm has a future in indexing, it remains to be
demonstrated, possibly at Glasgow (science goes slowly
from a congress to the next, even at Internet time).

Armel


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The problems of impurities in powder samples and indexing -
and the possibilty of reliable ("black box") powder indexing
method might be realisable Re: the recent work by the following:
Benson M. Kariuki, Scott A. Belmonte, Malcolm I. McMahon,
Roy L. Johnson, Kenneth D. M. Harris and Richard J. Nelmes in
the recent paper in J. Synchrotron Radiation, (1999), 6, pp 87-92.
"A new approach for indexing powder diffraction data
based on whole-profile fitting and global optimization using a
genetic alforithm".

This combines Le Bail whole pattern fitting with Genetic
Algorithms for the optimisation.  Hopefully there may be
an available software package to show this in action at
the Glasgow IUCr Software Fayre
     http://www.ccp14.ac.uk/projects/iucr99-softwarefayre/

In theory, overlapping peaks (not having wonderful
synchrotron data) might also not be that
big a problem; again, due to optimising on the whole
profile.

If this is a new robust method for powder indexing, it
would be a shame to see it just gathering dust in the
printed literture.   One perceived problem with new algorithms
for structure solution from powder diffraction data is that
many of them don't seem to make it beyond the printed word.

Though in the case of indexing, it sounds like the majority
of users must be happy with the combination of Ito, Treor,
Dicvol - otherwise - they would be taking the ideas in
the above and similar journal articles and converting it
to executable code post haste? (i.e., using Le Bail fitting
combined with an appropriate optimisation algorithm - or
suite of algorithms - of which the genetic algorithm seems
to be one of the more obvious ones to use as described in
the above reference)

---

As an extra aside - given the availability of Le Bail fitting
in most Rietveld software - optimising to give the best fit
for indexing might also give an option for automatic suggestion
of space groups.

Lachlan.

> Of course, proper indexation is the condition sine qua non.
> Ito, Dicvol and Treor are already extremely reliable. Using
> all of them ensure you evenmore success. The problem is
> that they work wonderfully only with wonderful data. I have
> heard about many other software and even recent use of
> Monte Carlo for indexing. That those software are more
> comfortable with bad starting data than Ito, Dicvol and Treor,
> I do not believe it. Then, the state of the art, in my opinion,
> continue to be the simultaneous use of Ito, Dicvol and Treor.
> The biggest problem on which you have little influence is
> your sample purity. Not being sure of the purity is sufficient
> for discouraging many researchers to adopt powder
> diffraction ;-).
>
> Armel
>
> Original mail :
> From: Gregory A Stephenson <STEPHENSON_GREGORY_A@...>
>
> >Although molecular finding methods may be considered a not so useful
technique
> >since "the structure" is already known from NMR or mass spectrometry (or a
> >chemist who actually has a reasonable idea of a few possibilities of what he
> >has synthesized-which is fortunately generally the case).  It still appears
to
> >me that in the event that you can rely on the latter, you still need the
basic
> >starting point-proper indexation.  I use the standard Ito, Dicvol and Treor
> >programs; each being very good-but indexation still seams to be more limiting
> >than the monte carlo/simulated annealing approach to solution.  What is the
> >state of the art?  Is there something more reliable than these programs for
> >low symmetry organic molecules?
>
>
> ------------------------------------------------------------------------
> Does your free web site address contain more letters than the alphabet?
> Register a domain name with DomainDirect. A domain with NO hosting fees.
> Visit http://clickhere.egroups.com/click/49 for full details.
>
>
> eGroup home: http://www.eGroups.com/group/sdpd
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>
>


--
Lachlan M. D. Cranswick

Collaborative Computational Project No 14 (CCP14)
     for Single Crystal and Powder Diffraction
Daresbury Laboratory, Warrington, WA4 4AD U.K
Tel: +44-1925-603703  Fax: +44-1925-603124
E-mail: l.cranswick@...  Ext: 3703  Room C14
NEW CCP14 Web Domain (Under heavy construction):
                            http://www.ccp14.ac.uk

Of course, proper indexation is the condition sine qua non.
Ito, Dicvol and Treor are already extremely reliable. Using
all of them ensure you evenmore success. The problem is
that they work wonderfully only with wonderful data. I have
heard about many other software and even recent use of
Monte Carlo for indexing. That those software are more
comfortable with bad starting data than Ito, Dicvol and Treor,
I do not believe it. Then, the state of the art, in my opinion,
continue to be the simultaneous use of Ito, Dicvol and Treor.
The biggest problem on which you have little influence is
your sample purity. Not being sure of the purity is sufficient
for discouraging many researchers to adopt powder
diffraction ;-).

Armel

Original mail :
From: Gregory A Stephenson <STEPHENSON_GREGORY_A@...>

>Although molecular finding methods may be considered a not so useful technique
>since "the structure" is already known from NMR or mass spectrometry (or a
>chemist who actually has a reasonable idea of a few possibilities of what he
>has synthesized-which is fortunately generally the case).  It still appears to
>me that in the event that you can rely on the latter, you still need the basic
>starting point-proper indexation.  I use the standard Ito, Dicvol and Treor
>programs; each being very good-but indexation still seams to be more limiting
>than the monte carlo/simulated annealing approach to solution.  What is the
>state of the art?  Is there something more reliable than these programs for
>low symmetry organic molecules?


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Although molecular finding methods may be considered a not so useful technique
since "the structure" is already known from NMR or mass spectrometry (or a
chemist who actually has a reasonable idea of a few possibilities of what he
has synthesized-which is fortunately generally the case).  It still appears to
me that in the event that you can rely on the latter, you still need the basic
starting point-proper indexation.  I use the standard Ito, Dicvol and Treor
programs; each being very good-but indexation still seams to be more limiting
than the monte carlo/simulated annealing approach to solution.  What is the
state of the art?  Is there something more reliable than these programs for
low symmetry organic molecules?



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We are now 113 subscribers to this mailing list.
It is timely for having some discussion, not only
announcing.

Recent success in determining structures from
scratch may suggest that a chemical analysis,
plus an indexed powder pattern would be sufficient
for a structure determination even if the Patterson
and direct methods fail. I mean that the molecular
structure may become unnecessary when dealing with
organic compounds. This implies that the work of
determining the molecular structure, which precede
necessarily the application of methods of molecule
location, becomes possibly useless. Investment
in a laboratory powder diffractometer is quite
less expensive than buying a big NMR. The recent
redetermination of the cimetidine structure from
scratch (a set of random positions as starting model),
by Monte Carlo process (with the Espoir software),
is quite encouraging. Moreover, the GNU license
authorizes you to hack this code at your convenience.
Nothing is better than Linux and the other open source
software on which independent and free workers are
heavily busy : this opinion is frequently presented in
most computer journals. Why not to do the same in
crystallography ?

Best

Armel Le Bail - Universite du Maine, Laboratoire des Fluorures,
CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France
http://www.cristal.org/


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ESPOIR is a Reverse Monte Carlo code for ab initio crystal
structure determination by fittting to "|Fobs|" extracted by
powder diffratometry.

The new release, ESPOIR 1.0, includes many new possibilities :

- Choosing any space group, not only P1.
- Annealing by reducing progressively the amplitude of atom moves.
- Accepting events that do not improve the fit that helps not getting
         trapped in false minima.
- Restarting automatically when false minima still exist.
- Optimization of the |F| calculation, saving time.
- New examples including the SDPD Round Robin sample I
   [Co(NH3)5CO3]NO3.H2O, and cimetidine C10H16N6S.

        http://www.cristal.org/sdpd/espoir/                  (USA)
or   http://pcb4122.univ-lemans.fr/sdpd/espoir/       (France)

Good luck !


Armel Le Bail - Universite du Maine, Laboratoire des Fluorures,
CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France
http://www.cristal.org/


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There is a new page on Available Powder Diffraction Indexing
Software and References (back to ~1980) at:

     http://www.ccp14.ac.uk/solution/indexing/

If there are any corrections, additions, etc for the
webpage  - please feel free to E-mail me.

Lachlan.

PS:  Does anyone know the availability, web-page or contact E-mail
address of the author for the  "Poroshok program complex"  -
software suite(?) for Powder Diffraction/Indexing for PC as stated in:
X-ray analysis using IBM-compatible personal computers", V.P. Serykh,
Industrial Laboratory, 1998, Vol.64, No.3, pp.158-161

Given the keyword of "full-profile" match the above paper and the
above author is also on: "Full-Profile Powder Patterns Indexing",
      V.P. Serykh, L.F. Verkhorobin,
      Kristallografiya, 1983, Vol.28, No.6, pp.1199-1200

It would be interesting to have a try on this software.

--
Lachlan M. D. Cranswick

Collaborative Computational Project No 14 (CCP14)
     for Single Crystal and Powder Diffraction
Daresbury Laboratory, Warrington, WA4 4AD U.K
Tel: +44-1925-603703  Fax: +44-1925-603124
E-mail: l.cranswick@...  Ext: 3703  Room C14
NEW CCP14 Web Domain (Under heavy construction):
                            http://www.ccp14.ac.uk

Information on the latest Update on the Endeavour Structure Solution
software from Powder Diffraction Data follows.  Lachlan.

=======================================

Bonn, April 28th 1999

NEWS FOR REGISTERED ENDEAVOUR USERS

As you may have already seen from our Homepage, the ENDEAVOUR software was
updated recently. It can be downloaded from
http://www.crystalimpact.com/endeavour/ .
It's not necessary to register again.


The current version 0.9.2 contains the following changes and/or
improvements:

- Use of selected Bragg reflections I(hkl) instead of powder diffraction
pattern I(2theta) possible (new command "loadhklexp").

- Electron diffraction (kinematic model only, no calculation of dynamic
diffraction).

- Several new examples: Al2O3 (Corundum), CaCO3 (Calcite, Aragonite),
Mg2SiO4, MgCu2, SiO2 (Cristobalite), TiO2 (Rutile).

- Corrected an error in the protocol file after the optimization: In the
comparison of calculated and observed intensities I(calc) and I(exp) were
exchanged in the tabular heading.

- License is valid until 31.05.99.


New features in version 0.9.1:

- Neutron diffraction data may now be used (new parameter "radiation").

- New parameter "2thetamin" may be used in combination with "2thetamax" to
select a range of reflections that are used during the calculation.

- Geometry of diffraction experiment may be chosen (Debye-Scherrer or
Guinier; new parameters "geometry", "guinangle", "guind").

- Maximum number of different atom types has been increased to 10.

- Corrected an error in the na3obr.inp sample file ("loadpksexp" replaced by
"loadpdiffexp").

- Corrected an error when reading PKS-files containing upper case letters.


So far these news. I hope, that ENDEAVOUR meets your expectations. If you
have any suggestions or comments, please feel free to contact me or Dr.
Holger Putz at putz@...

Best regards

Michael Berndt

###################################
Dr. Michael Berndt
CRYSTAL IMPACT
K.Brandenburg & M.Berndt GbR
Postfach 1251
D-53002 Bonn
Germany
Phone: +49 - 228 - 735825
Fax: +49 - 228 - 739586
E-Mail: berndt@...
URL: http://www.crystalimpact.com
###################################




--
Lachlan M. D. Cranswick

Collaborative Computational Project No 14 (CCP14)
     for Single Crystal and Powder Diffraction
Daresbury Laboratory, Warrington, WA4 4AD U.K
Tel: +44-1925-603703  Fax: +44-1925-603124
E-mail: l.cranswick@...  Ext: 3703  Room C14
NEW CCP14 Web Domain (Under heavy construction):
                            http://www.ccp14.ac.uk

Dear Subscribers,

On behalf MSI, this mail is for announcing the successful
solution of the sample II SDPD round robin structure by
the Powder Solve software (post-deadline).

With permission, the full report is available as a text file at :
      http://pcb4122.univ-lemans.fr/SDPDRR/part5.txt
or as a MS Word file compressed by Winzip at :
      http://pcb4122.univ-lemans.fr/SDPDRR/part5.zip

The use is not to disclose participant names if they do not
wish so. But if they wish, then why not. So that, if other
regular pre-deadline participants wish to disclose their
round robin report, please let us know. Anyway, a summary
of these results is still available at :
http://www.cristal.org/iniref/ecm18/ecm18sdpdrr.html

Best,

The SDPD Round Robin organizers
A. Le Bail and L Cranswick

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As announced last week, a special purpose Reverse Monte Carlo
code for ab initio crystal structure determination by fitting to
"|Fobs|" extracted  by powder diffractometry is available at :
                http://www.cristal.org/sdpd/espoir/

The source code is available under the GNU license.

Best wishes,


Armel Le Bail - Universite du Maine, Laboratoire des Fluorures,
CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France
http://www.cristal.org/


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L. Keller wrote:
>In a message dated 4/14/99 3:19:14 PM EST, finger@... writes:
>
>> If you banish me from the list, the punishment would be appropriate.
>>
>Grenoble is still asleep but I am afraid punishment will be harsh. I recommed
>you seek asylum in another list fast.

People sending source code are so rare nowadays that only
acknowledgements are appropriate. Larry has already found asylum
in the SDPD mailing list, at which a discussion about individual
peak fitting is certainly more appropriate than at the Rietveld list.

Subscribe by sending a mail to sdpd-subscribe@egroups.com
or visit http://www.cristal.org/sdpd/

Next week will be released a new RMC code able to determine
structures ab initio from "|Fobs|" extracted by powder diffractometry.
The program name is ESPOIR, however, you should not load too
much hope in it since the size of the structures easily determined
is not larger than 15-30 independent atoms in P1 spacegroup.
Moreover the development has taken less than one week, which
is not reassuring ;-)
The source code (Fortran) will be distributed on demand. The
executable will not have any vanishing date.:).

Anyway, the program will be located at a Web address where
it could be downloaded. No distribution by e-mail to the whole
list (I hope).

Cheers,

Armel Le Bail

P.S. "ESPOIR" in french means "hope" in english, something
not to lose when dealing with SDPD.


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Apologies if I am flooding too many mail boxes with
this but it may also be relevant to SDPD people for
helping generate starting/trial models from
exisiting structures due to the way the following
can transform in a quick and relatively user-friendly
way.

=================================

CRYSCON for Windows Shareware by Eric Dowty

A program that may be of interest for general
crystallographic structure/hkl/cell conversion
and those requiring Trial structures/starting models
is the "Shareware" CRYSCON for Windows software
by Eric Dowty (of ATOMS and SHAPE software fame).
This is presently a beta version but looks pretty
solid so far and will read in a variety of
file formats - including ICSD.

   http://www.tricon.net/comm/shape/#anchor_cryscon
UK Mirror:
   http://www.ccp14.ac.uk/ccp/web-mirrors/shape/comm/shape/#anchor_cryscon

--------

For instance, it fits in well with getting structure data
from the ICSD web (or ICSD CD-ROM) interfaces - cutting out
the results in ICSD format into a text file then importing
into Cryscon  (File, Import, ICSD Original).

    http://icsd.ccp14.ac.uk/icsd/
    http://rrdjazz.nist.gov/~toby/icsd/
    http://www.caos.kun.nl/icsd/
    http://sigma.numse.nagoya-u.ac.jp/dif/icsd/
And the master site on Alan Hewat's web area at
ILL in France:
    http://193.49.43.4/dif/icsd/
(Full database is available free for UK academics as
part of the CDS National Licence:
   http://www.dl.ac.uk/CDS/llicsd.html
though repeating myself from the Clay Minerals list,
the CDS based icsd search software still has the command
line edge on doing things such as searching on cell ratios)

------------

Blurb follows:
"CRYSCON  - general crystallographic conversion utility"

"You can convert to a sub-cell or super-cell or
simply translate to a different origin or interchange
axes; or any combination of these. You can convert
to a sub- or super- symmetry group, or even a
non-related space group . When converting to a
sub-cell or to higher symmetry the positions of
presumably coincident or superimposed atoms are
averaged, and when converting to a super-cell or
lower symmetry the extra symmetry-unique atoms
which may be required are generated. In any case the
result is a set of symmetry-unique atoms for the
target cell and symmetry, suitable for entry into
crystallographic software such as Fourier analysis,
least-squares refinement or structure drawing.

Other features include simulation of powder
diffractograms and precession photographs;
transformation and reorientation of anisotropic
temperature factors and magnetic or other vectors;
computation of bond lengths and angles; and
transformation of (hkl) index data, such as
diffraction data."

============
=============

Lachlan.

--
Lachlan M. D. Cranswick

Collaborative Computational Project No 14 (CCP14)
     for Single Crystal and Powder Diffraction
Daresbury Laboratory, Warrington, WA4 4AD U.K
Tel: +44-1925-603703  Fax: +44-1925-603124
E-mail: l.cranswick@...  Ext: 3703  Room C14
NEW CCP14 Web Domain (Under heavy construction):
                            http://www.ccp14.ac.uk

Dear Members,

There are currently 83 subscribers to the SDPD Mailing List.

This mail to say that not only the pharmaceutical sample
2 of the SDPD Round Robin could have been solved by
DIRDIF, by using the ORIENT option that locate a known
fragment.

For sample 1 also, it was possible easily to guess the
existence of at least a [CoN5O] octahedron from the given
formula [Co(NH3)5CO3]NO3.H2O. Building such an
octahedron inside the ORUSER base of fragments is
quite easy. I have verified that DIRDIF was able to locate
this octahedron, regardless of the O position, from either
the full dataset of structure factors as extracted by FULLPROF
or any reduced dataset built by excluding reflections having
a neighbouring one at less that 0.05 2-theta degrees. Those
data are available at :
        http://www.cristal.org/SDPDRR/sample1.html

Supplementary atoms are proposed by the DIRDIF Fourier
synthese, so that an uncomplete solution is built that provides a
Rietveld RB factor as low as 20%, sufficient for refining
and going to the complete solution by further Fourier
difference syntheses.

Of course, a CO3 group attached to this octahedron with
the possibility to vary their relative orientations would have
been better. And also, adding a second fragment like NO3
plus a water molecule would have even completed the
structure. Unfortunately, this is not yet possible with the
DIRDIF software, accepting only one fragment.
Anyway, DIRDIF worked well on this case !

Still no more sophisticated software for molecule location
available on the market, apart Cerius2 ???

Best regards,


Armel Le Bail - Universite du Maine, Laboratoire des Fluorures,
CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France
http://www.cristal.org/


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> I would like to know if exists a software devoted to the indexation of
> superstructure lines in a powder pattern.
>
> i.e. : I have a powder pattern and managed to index (by analogy with a known
> structure) the majority of the lines. I have some remaining unindexed lines
> and am pretty sure that they do not belong to an additional phase.
>         I wonder if exists some software taking into account (contrary to
> the usual indexation programs like dicvol, treor) the cell already indexed
> and trying to index the remaining lines in a supercell automatically.
>

Has you tried the following:
   Program: SUPERCELL  (J.Rodriguez-Carvajal, LLB-December-1998)

"This program can be used to index superstructure reflections from
   a powder diffraction pattern. The program needs "nobs" observations
   (angular positions of satellite peaks) to work. The variable nobs is
   limited to a maximum of 40."
FIRST APPROACH
   The first approach consist in searching the best "unit cell"
   compatible with a set of SUPERSTRUCTURE observed lines in powder
   diffraction.
SECOND APPROACH
   If the first approach fails to give a suitable solution the superstructure
   may be inconmensurate and a direct search for the propagation vector and
   one of its harmonics have to be used.

This is downloadable off the original French site and mirrors.

This comes with the Winplotr software for Windows
   http://www-llb.cea.fr/winplotr/winplotr.htm
   http://www.ccp14.ac.uk/ccp/web-mirrors/plotr/winplotr/winplotr.htm
  
ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/plotr/plotr/p\
lotr.htm

   ftp://bali.saclay.cea.fr/pub/divers/winplotr/
   http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/fullprof/pub/divers/winplotr/
  
ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/ccp14/ftp-mirror/fullprof\
/pub/divers/winplotr/

---

Another option is to use Brian Toby's CMPR software for
manual indexing which I am told is very nifty in this
area.  I have only used it myself with trivial
cells.  As you have a cell of sorts, you can then
interactively use slide bars to be visually trying to
sort out the reflections without the nuances of the
automated programs(?).

Refer:
   http://www.ccp14.ac.uk/tutorial/cmpr/index.html

Lachlan.

>
> ---------------------------------------------------------------
> Jean-Marc Joubert
> Laboratoire de Chimie Metallurgique des Terres Rares
> CNRS -  UPR 209
> 2-8 rue Henri DUNANT,
> 94320 THIAIS CEDEX - FRANCE
>
> Phone: 33 (0)1 49 78 12 11
> Fax:    33 (0)1 49 78 12 03
>
> Email:  joubert@...


--
Lachlan M. D. Cranswick

Collaborative Computational Project No 14 (CCP14)
     for Single Crystal and Powder Diffraction
Daresbury Laboratory, Warrington, WA4 4AD U.K
Tel: +44-1925-603703  Fax: +44-1925-603124
E-mail: l.cranswick@...  Ext: 3703  Room C14
NEW CCP14 Web Domain (Under heavy construction):
                            http://www.ccp14.ac.uk

Jean-Marc Joubert
>
>I would like to know if exists a software devoted to the indexation of
>superstructure lines in a powder pattern.
>
>i.e. : I have a powder pattern and managed to index (by analogy with a known
>structure) the majority of the lines. I have some remaining unindexed lines
>and am pretty sure that they do not belong to an additional phase.
>        I wonder if exists some software taking into account (contrary to
>the usual indexation programs like dicvol, treor) the cell already indexed
>and trying to index the remaining lines in a supercell automatically.

I never heard about such a special software. However, the best adapted
existing indexing program is Dicvol, certainly. Due to the exhaustivity
of the search performed by Dicvol, and to the fact that no unindexed
line is tolerated, if you have already a set of indexed lines, then, just
adding
one line doubling (or multiplying by any value) any axis, and Dicvol
will find the superstructure. You cannot expect that from Treor
or Ito as systematically as with Dicvol.

Hope this helps,

Armel Le Bail - Universite du Maine, Laboratoire des Fluorures,
CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France
http://www.cristal.org/


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I would like to know if exists a software devoted to the indexation of
superstructure lines in a powder pattern.

i.e. : I have a powder pattern and managed to index (by analogy with a known
structure) the majority of the lines. I have some remaining unindexed lines
and am pretty sure that they do not belong to an additional phase.
         I wonder if exists some software taking into account (contrary to
the usual indexation programs like dicvol, treor) the cell already indexed
and trying to index the remaining lines in a supercell automatically.

Thank you.

---------------------------------------------------------------
Jean-Marc Joubert
Laboratoire de Chimie Metallurgique des Terres Rares
CNRS -  UPR 209
2-8 rue Henri DUNANT,
94320 THIAIS CEDEX - FRANCE

Phone: 33 (0)1 49 78 12 11
Fax:    33 (0)1 49 78 12 03

Email:  joubert@...


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Zhu Jianghai wrote:
>    I am very interested in this. I will try it. I want to know more about
>Simulated Annealing and Pareto-optimization. Where can I find some
>papers on these theroies?

About Pareto : 265 papers are listed at UnCover Web and 843
papers are suggested when using the "simulated annealing"
keywords.
             http://uncweb.carl.org/

At INIST-CNRS, 117 papers are found with "pareto" in the title
and 545 papers with "simulated annealing"
           http://www.inist.fr/

No paper combining the 3 keywords was found. You may
consider to wait for a paper submitted by Putz et al. to
J. Appl. Cryst., announced as giving a detailed description.

Concerning SDPD, the review paper which writes may be
the more about Monte Carlo could be :
Crystal structure determination from powder diffraction data ?
Harris KDM. Tremayne M.
Chemistry of Materials. 8 (1996) 2554-2570.

And many are available at the SDPD Database, for instance
in the special methods Web page :
       http://www.cristal.org/iniref/spemeth.html

Searching by keywords among experimental cases at :
      http://pcb4122.univ-lemans.fr/cgi-bin/iniref.pl
gives 3 papers with "simulated annealing" and 9 papers
with "Monte Carlo", one paper with "global optimization".

Note that, there is no way to enter a constrained molecule
into Endeavour 0.9.1, and that any problem is treated in P1
space group, up to now. Many unavailable or commercial
software can do better, in principle, although none solved
the SDPD Round Robin sample 1 structure in due time, nor
after the deadline.

Best wishes

Armel Le Bail - Universite du Maine, Laboratoire des Fluorures,
CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France
http://www.cristal.org/


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Hi,
     I am very interested in this. I will try it. I want to know more about
Simulated Annealing and Pareto-optimization. Where can I find some
papers on these theroies?

     Best regards.

Zhu Jianghai




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Dear SDPD Mailing List Members,

Two weeks ago, I have tried the new Endeavour 0.9
software, which uses simulated annealing.
http://www.crystalimpact.com/endeavour/Default.htm

Because the authors solved structures with up to 116
independent atoms in the unit cell, it does not seemed
impossible to manage the SDPD Round Robin sample 1
with its 30 non-hydrogen atoms, by using simple
repulsion potentials based on minimum interatomic
distances.

I failed, either from extracted Intensities or from exact
ones (and I would be happy if somebody could show
me how to succeed). But the 0.9 Endeavour version
was limited to 4 atom-kinds maximum. This corresponds
to the number of different non-hydrogen atoms in
the cobalt amine [Co(NH3)5]CO3.NO3.H2O, but
this was unsufficient for a differentiation of two
kinds of N atoms (Co-N and NO3), and four kinds
of O atoms (Co-O-C, O-C, O-N in NO3 and O-H
in H2O). Anyway, there were encouraging clues
so as the fact that the two Co atoms as well as the
two C atoms were showing a y+1/2 relation
corresponding well to the P21 expected space group.
But no CoN5O octahedra, no CO3 or NO3 groups
were built.

So that I am now trying Endeavour 0.9.1 which can
handle problems with up to 10 atom-kinds.
Calculations progress slowly on my Pentium II
333 Mhz.

I would be interested in hearing success story with
this new software. Those willing to test the program
with the SDPD Round Robin sample 1 data may
download them at :
  http://pcb4122.univ-lemans.fr/sdpd/data/endeav-1.zip
Maybe my choices of minimum interatomic distances
are inadequates.

Any hint ?

Best wishes,

Armel Le Bail - Universite du Maine, Laboratoire des Fluorures,
CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France
http://www.cristal.org/


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http://www.icdd.com/ppxrdsymp/ works for me.
What web browser are you using?

I don't have a problem with getting there - though
I am on a very good internet link.
They also do seem to have a   <noframes> tag for old
browsers so this should be working on the pre-frames
browsers and it does on my "pre-frame" test
web browser.  If links are a problem I can ask to have
the ICDD pages mirrored at CCP14 in Europe.

Lachlan.

>
> Hi Lachlan,
> can you really connect to ICDD's server ? I've been getting "Zero sized
> reply" back for days now.
> Best wishes,
> Lubo
>
> On Sat, 27 Mar 1999, L. Cranswick wrote:
>
> >
> > Sent on behalf of the ICDD - International Centre for Diffraction Data
> >                    (http://www.icdd.com)
> >
> > Pharmaceutical Powder Diffraction Symposium (PPXRD) - September 1999, USA
> >
> > The ICDD, with Glaxo Wellcome co-sponsership, is organizing a three-day
> > symposium
> > dedicated to the use of X-ray diffraction for pharmaceutical applications.
> > The Pharmaceutical Powder Diffraction Symposium (PPXRD) will be held at ICDD
> > headquarters in Newtown Square, Pennsylvania, USA on September 27-29, 1999.
> >
> > Sessions will include:
> >   I.    XRD Applications in Pre-formulation and Formulation
> >   II.   Non-Ambient XRD Applications in Pharmaceuticals
> >   III.  Crystallinity and Crystal Form Quantification Including Rietveld
> >         Applications
> >   IV.   Structure Determination, Indexing and Molecular Modeling
> >   V.    Patents/Regulatory Issues
> >
> > More Information can be obtained on the web at:
> >                      http://www.icdd.com/ppxrdsymp/
> >
> > For any queries, E-mail ppxrd@....
> >
> >
> >
> >
> >
>


--
Lachlan M. D. Cranswick

Collaborative Computational Project No 14 (CCP14)
     for Single Crystal and Powder Diffraction
Daresbury Laboratory, Warrington, WA4 4AD U.K
Tel: +44-1925-603703  Fax: +44-1925-603124
E-mail: l.cranswick@...  Ext: 3703  Room C14
NEW CCP14 Web Domain (Under heavy construction):
                            http://www.ccp14.ac.uk

Hi Lachlan,
can you really connect to ICDD's server ? I've been getting "Zero sized
reply" back for days now.
Best wishes,
Lubo

On Sat, 27 Mar 1999, L. Cranswick wrote:

>
> Sent on behalf of the ICDD - International Centre for Diffraction Data
>                    (http://www.icdd.com)
>
> Pharmaceutical Powder Diffraction Symposium (PPXRD) - September 1999, USA
>
> The ICDD, with Glaxo Wellcome co-sponsership, is organizing a three-day
> symposium
> dedicated to the use of X-ray diffraction for pharmaceutical applications.
> The Pharmaceutical Powder Diffraction Symposium (PPXRD) will be held at ICDD
> headquarters in Newtown Square, Pennsylvania, USA on September 27-29, 1999.
>
> Sessions will include:
>   I.    XRD Applications in Pre-formulation and Formulation
>   II.   Non-Ambient XRD Applications in Pharmaceuticals
>   III.  Crystallinity and Crystal Form Quantification Including Rietveld
>         Applications
>   IV.   Structure Determination, Indexing and Molecular Modeling
>   V.    Patents/Regulatory Issues
>
> More Information can be obtained on the web at:
>                      http://www.icdd.com/ppxrdsymp/
>
> For any queries, E-mail ppxrd@....
>
>
>
>
>


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Sent on behalf of the ICDD - International Centre for Diffraction Data
                    (http://www.icdd.com)

Pharmaceutical Powder Diffraction Symposium (PPXRD) - September 1999, USA

The ICDD, with Glaxo Wellcome co-sponsership, is organizing a three-day
symposium
dedicated to the use of X-ray diffraction for pharmaceutical applications.
The Pharmaceutical Powder Diffraction Symposium (PPXRD) will be held at ICDD
headquarters in Newtown Square, Pennsylvania, USA on September 27-29, 1999.

Sessions will include:
   I.    XRD Applications in Pre-formulation and Formulation
   II.   Non-Ambient XRD Applications in Pharmaceuticals
   III.  Crystallinity and Crystal Form Quantification Including Rietveld
         Applications
   IV.   Structure Determination, Indexing and Molecular Modeling
   V.    Patents/Regulatory Issues

More Information can be obtained on the web at:
                      http://www.icdd.com/ppxrdsymp/

For any queries, E-mail ppxrd@....

Dear Members,

Already 57 subscribers to the SDPD Mailing List, 36 hours
after its birth. This may be considered as quite encouraging !

Unfortunately for you, descriptions of efforts in trying to
succeed in a SDPD may be really boring. I hope that you are
prepared to read long emails ! Here is the first one :-).

Since the SDPD Round Robin deadline, one of my constant
preoccupation is to try to demonstrate that the two
structures were not so difficult to determine from the
provided data (which were not presenting the highest
resolution possible, otherwise there would have been
no challenge at all).

About the pharmaceutical sample, tetracycline hydrochloride,
you may remember that 2 participants of the Round Robin
were able to solve it. One by the Global Optimization
Method for molecule location (DRUID software), and the
other by Patterson method, using the CSD package. The
SDPD Round Robin organizers were also able to solve
the structure by using PATSEE.
For the SDPDRR see :
     http://www.cristal.org/SDPDRR/

From my quest in order to find available software able
to solve this problem easily, I have one to present today :
DIRDIF. It is a freeware, distributed with source code
at :    http://www-sci.sci.kun.nl/xtal/dirdif/dirdif.html

DIRDIF, from Prof. Paul T. Beurskens and co-workers is a
computer  program system for crystal structure determination by
Patterson  methods and direct methods applied to difference
structure factors.  Versions are available for a wide range of
computer and  operating systems. They have been tested and
used on IBM/cms,  VAX/VMS, CYBER computer, PC (PCDOS,
MSDOS) and various unix systems (Silicon Graphics, SunOS,
Solaris, DEC, Alpha, HP, linux, IBM/AIX).

A MS Windows version, built by Louis Farrugia, is available
at :         http://www.chem.gla.ac.uk/~louis/software/

None of the 31 participants (of 72) having answered to the
questions concerning how they intended to solve the SDPD
Round Robin sample structures suggested DIRDIF ! This
means that DIRDIF is not well known by our community,
and indeed I ignored myself what could be its capacities
till last week...

Owing to the poor resolution data, it is clear that methods
allowing to use knowledge of the molecular structure have
an advantage here. This is the case of DIRDIF presenting
an option for structures of molecules with (partly) known
geometry.

Once identified that the C22H24N2O8.HCl was undoubtedly
built from the very well known tetracycline molecule (looking
inside CSD or interrogating Internet, or chemical company
catalogs, for instance), all the DIRDIF user has to do is to
insert the model inside a file gathering molecular fragments,
if it is not already included (ORBASE and ORUSER files).

For the SDPDRR sample 2, I used the tetracycline molecule
as provided in the TETCYH10 CSD entry, which is the
hexahydrate (the same was used by the DRUID team). The
data in the .mol2 file built at the end of  a CSD query were
inserted in the DIRDIF ORUSER file, excluding the water
molecules, of course. Then, I used the DOS DIRDIF version
(quite easy to install), after having prepared a INS and a
HKL files (both SHELX -like, the latter from a Le Bail
method structure factor extraction from the synchrotron
data, with application of the OVERLAP software in order
to exclude reflections having neighbouring ones at less
than 0.005 2-theta degrees - yes, no error - synchrotron
data ;-).

I really found the DIRDIF manual clear, there is an
example provided, and typical runs are described. For
obtaining the molecule location, the sequence of orders
at the command line are (neglecting some questions/
answers):

DIRDIF TETRAC PATTY
This produces Patterson search. Examining the result shows
that the Cl atom is located, but the further efforts of DIRDIF
in order to propose a model are not very convincing. Only 2
files are called here (INS and HKL). TETRAC is an
arbitrary chosen name.

DIRDIF TETRAC ORBASE
This will prepare data including the tetracycline fragment
entered previously in ORUSER.

DIRDIF TETRAC ORIENT
This will execute the search for molecule location/orientation

One of the location proposition is used by DIRDIF for
trying to find the lacking atoms. DIRDIF successfully
locates the Cl atom. However, you may have to disregard
the final rearrangements of atoms proposed after several
Fourier syntheses, and preferably look at the coordinates
of the molecule as oriented (and not further distorted).

A Zipped file containing the three files (INS, HKL and
ORUSER) which will allow you to reproduce my efforts is
available at :
     http://pcb4122.univ-lemans.fr/sdpd/data/dirdif-1.zip
The file contains also atold (summary of DIRDIF propositions)
as well as dirdif.pcr and dirdif.dat which would
allow you to verify that the raw model provided by DIRDIF
leads to Rp =32%, RF = 16.4%, by using FULLPROF on the
SDPD Round Robin synchrotron data, a quite good starting
model for subsequent refinements, no ?

Some words about the Louis Farrugia Windows version.
There is a bug making that the ORIENT version is not
working. Louis is currently busy on that question. Wait
before downloading. But the DOS version works quite
fine.

All the best, and have fun with DIRDIF.

Thanks to the DIRDIF team for making available the
whole package in the old good Academic way (including
sources, so that the curious may understand more) !


Armel Le Bail - Universite du Maine, Laboratoire des Fluorures,
CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France
http://www.cristal.org/


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Structure Determination by Powder Diffractometry (SDPD) is hot, as evidenced by
the continuous flow of new software appearing, academic as well as commercial.
Sharing experiences is the target of this unmoderated mailing list maintained by
Armel Le Bail and Lachlan Cranswick. Join us and enjoy !

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