RE: structure solution terminology

[Khalifah, Peter]

Dear Arie,

I would argue that this distinction between electron density and atomic form 
factors represents an important difference in method.  

If you have good single crystal data on a compound with covalent bonding, you 
will see that the electron density significantly differs from the spherical 
density that is assumed if you use atomic form factors to describe the system.  
Similarly, in inorganic solid state compounds, one often runs across systems in 
which atoms are split over multiple sites, or where stacking faults cause the 
average electron density at a discrete atomic site to be only a few percent of 
that of the full atom.  

Methods like charge flipping can readily deal with these deviations from 
expectations since the electron density is directly manipulated.  Methods which 
simply shuffle atoms (with fixed form factors) often cannot, though there are 
of course some model-dependent methods of dealing with this problem (varying 
site occupancies, artificially substituting heavy atoms with multiple lighter 
atoms, pre-splitting atomic sites, etc.).

To come back to Lubo's questions, it seems like the answer needs a lot of 
qualifiers to meet the mixture of general and specific classifications that 
responders have contributed.  One way of expressing this could be "Structure 
solution by serial trial model refinement".

"Serial" indicates that there is no relationship between the "trial models" (as 
there would be in a genetic algorithm), and "refinement" indicates that each 
initial trial model is optimized by standard Rietveld refinement methods.  The 
words "random guessing" are omitted even though that is what the method does, 
as this may help keep manuscripts from getting dinged.  "Serial" could be 
replaced by "RMC", "genetic algorithm", or "simulated annealing" if there was a 
relationship between the parameters within the different trial models.

Best wishes,

Peter

Dr. Peter Khalifah, kp...@bnl.gov

Associate Professor            Chemist 
Dept. of Chemistry             Dept. of Chemistry 
Stony Brook University         Brookhaven National Laboratory 
Stony Brook, NY 11794-3400     Upton, NY 11973-5000 
  
Office: 447 Grad. Chemistry    Office: Bldg 555, Rm 340 
Phone: (631)632-7796           Phone: (631)344-7689 
Fax: (631)632-7960             Fax: (631)344-5815
Web page: https://sites.google.com/a/stonybrook.edu/pgk/home
 





-Original Message-
From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf Of 
A. van der Lee
Sent: Thursday, December 17, 2015 10:58 AM
To: rietveld_l@ill.fr
Subject: Re: structure solution terminology

Lubomir Smrcok wrote the following on 17/12/2015 16:48:
> Sorry,
>
> Arie, genetic algorithm (or its relatives) does not shuffle electron 
> density, just atom coordinates.

And with the atom coordinates the electron density is shuffled, not?
The unit cell electron density is just the convolution of the atomic 
coordinates with spherical or non-spherical electron densities centered on each 
atom (3D) coordinate.
Arie
>Taking them the procedure (not GA
> itself) calculates structure factors and compares them to the "observed"
> structure factors (their squares, or intensities). Decision making  
>process of GA is not based on the differences in electron density, but  
>on |Fo|^2-|Fc|^2.
>
> Lubo
>
>
> On Thu, 17 Dec 2015, A. van der Lee wrote:
>
>> I agree with Yaroslav Filinchuk's thoughts:
>>
>> "However, the "structure solution in direct space" does not attempt 
>> to work in the reciprocal space - all the manipulations are done in 
>> the direct space."
>>
>> RMC, normal MC, genetic algorithms, they all shuffle electron density 
>> in some or another way in real space. So 'real space structure 
>> solution' sounds the best, and 'real space' is better than 'direct 
>> space' as to avoid confusion with 'direct methods'.
>>
>> Arie
>> ps: we should propose a new possible data value for 
>> _atom_sites_solution_primary By the way the data value vecmap 
>> (real-space vector search) is, I suppose, equivalent to a real-space 
>> Patterson search, which is indeed not the same as RMC, normal MC, 
>> genetic algorithms or other shuffle methods.
>>
>>
>> Mike Glazer wrote the following on 17/12/2015 12:50:
>>> But the original question was:
>>> What's the right nickname for the method of structure solution from 
>>> powders, which instead of analyzing electron (nuclear) density 
>>> shuffles atoms or molecules around a cell and compares experimental 
>>> and calculated patterns ?
>>> That's what we do with RMC in practice. We use RMC to create models 
>>> and then compare with experimental patterns.
>>> Mike
>>>
>>> Professor A M Glazer
>>> Department of Physics
>>> Parks Road
>>> Oxford
>>> OX1 3PU
>>> United Kingdom
>>> Tel/Fax: 44 1865 272290
>>> Mobile: 0778 696 0537
>>> **
>>> Vice-President of the International Union of Crystallography 
>>> Emeritus Professor of Physics and Emeritus  Fel

Re: structure solution terminology

[A. van der Lee]

Lubomir Smrcok wrote the following on 17/12/2015 16:48:

Sorry,

Arie, genetic algorithm (or its relatives) does not shuffle electron
density, just atom coordinates.


And with the atom coordinates the electron density is shuffled, not?
The unit cell electron density is just the convolution of the atomic 
coordinates with spherical or non-spherical electron densities centered 
on each atom (3D) coordinate.

Arie

Taking them the procedure (not GA
itself) calculates structure factors and compares them to the "observed"
structure factors (their squares, or intensities). Decision making
process of GA is not based on the differences in electron density, but
on |Fo|^2-|Fc|^2.

Lubo


On Thu, 17 Dec 2015, A. van der Lee wrote:


I agree with Yaroslav Filinchuk's thoughts:

"However, the "structure solution in direct space" does not attempt to
work in the reciprocal space - all the manipulations are done in the
direct space."

RMC, normal MC, genetic algorithms, they all shuffle electron density
in some or another way in real space. So 'real space structure
solution' sounds the best, and 'real space' is better than 'direct
space' as to avoid confusion with 'direct methods'.

Arie
ps: we should propose a new possible data value for
_atom_sites_solution_primary
By the way the data value vecmap (real-space vector search) is, I
suppose, equivalent to a real-space Patterson search, which is indeed
not the same as RMC, normal MC, genetic algorithms or other shuffle
methods.


Mike Glazer wrote the following on 17/12/2015 12:50:

But the original question was:
What's the right nickname for the method of structure solution from
powders, which instead of analyzing electron (nuclear) density
shuffles atoms or molecules around a cell and compares experimental
and calculated patterns ?
That's what we do with RMC in practice. We use RMC to create models
and then compare with experimental patterns.
Mike

Professor A M Glazer
Department of Physics
Parks Road
Oxford
OX1 3PU
United Kingdom
Tel/Fax: 44 1865 272290
Mobile: 0778 696 0537
**
Vice-President of the International Union of Crystallography
Emeritus Professor of Physics and
Emeritus  Fellow of Jesus College Oxford
Visiting Professor at the University of Warwick
Crystallographer
**
" Je ne te parlerai que cristaux" L. Pasteur (1850)


http://ukcatalogue.oup.com/product/9780198744306.do


-Original Message-
From: Radovan Cerny [mailto:radovan.ce...@unige.ch]
Sent: 17 December 2015 11:03
To: Mike Glazer ; Lubomir Smrcok
; Leonid Solovyov 
Cc: rietveld_l@ill.fr
Subject: RE: structure solution terminology

RMC covers only a part of the "Direct space methods", not for example
methods using evolution algorithms.


Radovan Cerny
Laboratoire de Cristallographie, DQMP
Universit? de Gen?ve
24, quai Ernest-Ansermet
CH-1211 Geneva 4, Switzerland
Phone  : [+[41] 22] 37 964 50, FAX : [+[41] 22] 37 961 08 mailto :
radovan.ce...@unige.ch
URL: http://www.unige.ch/sciences/crystal/cerny/rcerny.htm


-Message d'origine-
De : rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] De
la part de Mike Glazer Envoy? : jeudi 17 d?cembre 2015 11:49 ? :
Lubomir Smrcok; Leonid Solovyov Cc : rietveld_l@ill.fr Objet : RE:
structure solution terminology

This all sounds like Reverse MonteCarlo (RMC) modelling. We have used
this with PDF analysis.
Mike Glazer



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--
**
A. van der Lee
Institut Europ?en des Membranes
CNRS - UMR 5635
Universit? de Montpellier II - Case Courrier 047
Place E. Bataillon
34095 MONTPELLIER Cedex 5 - FRANCE

Tel : 33 (0) 4 67 14 91 35
Fax : 33 (0) 4 67 14 91 19

**
member of RECIPROCS - R?seau des Enseignants, Chercheurs et ITA
Professionnels de la Cristallographie Structurale (French professional
crystallographer network):
http://metiersit.dsi.cnrs.fr/index.php?page=ReseauMetiers&codeBap=B
**




--
**
A. van der Lee
Institut Européen des Membranes
CNRS - UMR 5635
Université de Montpellier II - Case Courrier 047
Place E. Bataillon
34095 MONTPELLIER Cedex 5 - FRANCE

Tel : 33 (0) 4 67 14 91 35
Fax : 33 (0) 4 67 14 91 19

**
member of RECIPROCS - Réseau des Enseignants, Chercheurs et ITA
Professionnels de la Cristallographie Structurale (French professional
crystallographer network):
http://metiersit.dsi.cnrs.fr/index.php?page=Reseau

RE: structure solution terminology

[Lubomir Smrcok]

In fact, one could agree with you. The problem is that RMC name has 
already been reserved, maybe even patented  :-)

Best wishes,
Lubo


On Thu, 17 Dec 2015, Mike Glazer wrote:


But the original question was:
What's the right nickname for the method of structure solution from powders, 
which instead of analyzing electron (nuclear) density shuffles atoms or 
molecules around a cell and compares experimental and calculated patterns ?
That's what we do with RMC in practice. We use RMC to create models and then 
compare with experimental patterns.
Mike

Professor A M Glazer
Department of Physics
Parks Road
Oxford
OX1 3PU
United Kingdom
Tel/Fax: 44 1865 272290
Mobile: 0778 696 0537
**
Vice-President of the International Union of Crystallography
Emeritus Professor of Physics and
Emeritus  Fellow of Jesus College Oxford
Visiting Professor at the University of Warwick
Crystallographer
**
" Je ne te parlerai que cristaux" L. Pasteur (1850) 



http://ukcatalogue.oup.com/product/9780198744306.do


-Original Message-
From: Radovan Cerny [mailto:radovan.ce...@unige.ch]
Sent: 17 December 2015 11:03
To: Mike Glazer ; Lubomir Smrcok ; 
Leonid Solovyov 
Cc: rietveld_l@ill.fr
Subject: RE: structure solution terminology

RMC covers only a part of the "Direct space methods", not for example methods 
using evolution algorithms.


Radovan Cerny
Laboratoire de Cristallographie, DQMP
Universit? de Gen?ve
24, quai Ernest-Ansermet
CH-1211 Geneva 4, Switzerland
Phone  : [+[41] 22] 37 964 50, FAX : [+[41] 22] 37 961 08 mailto : 
radovan.ce...@unige.ch
URL: http://www.unige.ch/sciences/crystal/cerny/rcerny.htm


-Message d'origine-
De : rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] De la part de 
Mike Glazer Envoy? : jeudi 17 d?cembre 2015 11:49 ? : Lubomir Smrcok; Leonid 
Solovyov Cc : rietveld_l@ill.fr Objet : RE: structure solution terminology

This all sounds like Reverse MonteCarlo (RMC) modelling. We have used this with 
PDF analysis.
Mike Glazer


++
Please do NOT attach files to the whole list 
Send commands to  eg: HELP as the subject with no body text
The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/
++

Re: structure solution terminology

[Lubomir Smrcok]

Sorry,

Arie, genetic algorithm (or its relatives) does not shuffle electron 
density, just atom coordinates. Taking them the procedure (not GA itself) 
calculates structure factors and compares them to the "observed" structure 
factors (their squares, or intensities). Decision making process of GA is 
not based on the differences in electron density, but on |Fo|^2-|Fc|^2.


Lubo


On Thu, 17 Dec 2015, A. van der Lee wrote:


I agree with Yaroslav Filinchuk's thoughts:

"However, the "structure solution in direct space" does not attempt to
work in the reciprocal space - all the manipulations are done in the
direct space."

RMC, normal MC, genetic algorithms, they all shuffle electron density in some 
or another way in real space. So 'real space structure solution' sounds the 
best, and 'real space' is better than 'direct space' as to avoid confusion 
with 'direct methods'.


Arie
ps: we should propose a new possible data value for 
_atom_sites_solution_primary
By the way the data value vecmap (real-space vector search) is, I suppose, 
equivalent to a real-space Patterson search, which is indeed not the same as 
RMC, normal MC, genetic algorithms or other shuffle methods.



Mike Glazer wrote the following on 17/12/2015 12:50:

But the original question was:
What's the right nickname for the method of structure solution from 
powders, which instead of analyzing electron (nuclear) density shuffles 
atoms or molecules around a cell and compares experimental and calculated 
patterns ?
That's what we do with RMC in practice. We use RMC to create models and 
then compare with experimental patterns.

Mike

Professor A M Glazer
Department of Physics
Parks Road
Oxford
OX1 3PU
United Kingdom
Tel/Fax: 44 1865 272290
Mobile: 0778 696 0537
**
Vice-President of the International Union of Crystallography
Emeritus Professor of Physics and
Emeritus  Fellow of Jesus College Oxford
Visiting Professor at the University of Warwick
Crystallographer
**
" Je ne te parlerai que cristaux" L. Pasteur (1850)


http://ukcatalogue.oup.com/product/9780198744306.do


-Original Message-
From: Radovan Cerny [mailto:radovan.ce...@unige.ch]
Sent: 17 December 2015 11:03
To: Mike Glazer ; Lubomir Smrcok 
; Leonid Solovyov 

Cc: rietveld_l@ill.fr
Subject: RE: structure solution terminology

RMC covers only a part of the "Direct space methods", not for example 
methods using evolution algorithms.



Radovan Cerny
Laboratoire de Cristallographie, DQMP
Universit? de Gen?ve
24, quai Ernest-Ansermet
CH-1211 Geneva 4, Switzerland
Phone  : [+[41] 22] 37 964 50, FAX : [+[41] 22] 37 961 08 mailto : 
radovan.ce...@unige.ch

URL: http://www.unige.ch/sciences/crystal/cerny/rcerny.htm


-Message d'origine-
De : rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] De la 
part de Mike Glazer Envoy? : jeudi 17 d?cembre 2015 11:49 ? : Lubomir 
Smrcok; Leonid Solovyov Cc : rietveld_l@ill.fr Objet : RE: structure 
solution terminology


This all sounds like Reverse MonteCarlo (RMC) modelling. We have used this 
with PDF analysis.

Mike Glazer



++
Please do NOT attach files to the whole list 
Send commands to  eg: HELP as the subject with no body 
text
The Rietveld_L list archive is on 
http://www.mail-archive.com/rietveld_l@ill.fr/

++




--
**
A. van der Lee
Institut Europ?en des Membranes
CNRS - UMR 5635
Universit? de Montpellier II - Case Courrier 047
Place E. Bataillon
34095 MONTPELLIER Cedex 5 - FRANCE

Tel : 33 (0) 4 67 14 91 35
Fax : 33 (0) 4 67 14 91 19

**
member of RECIPROCS - R?seau des Enseignants, Chercheurs et ITA
Professionnels de la Cristallographie Structurale (French professional
crystallographer network):
http://metiersit.dsi.cnrs.fr/index.php?page=ReseauMetiers&codeBap=B
**

++
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++

Re: structure solution terminology

[Alan Hewat]

>
> Brute force is a nicer way of putting it than blind luck :-)


Does "Tour de force" work in American ?

I have had that get by US reviewers, though they otherwise correct my
English :-)

Alan.
__
*   Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE *
 +33.476.98.41.68
http://www.NeutronOptics.com/hewat
__
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++

RE: structure solution terminology

[Whitfield, Pamela S.]

How about 'brute force with some educated guesswork'!
Brute force is a nicer way of putting it than blind luck :-)

See how that goes with reviewers!

Pam

-Original Message-
From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf Of 
A. van der Lee
Sent: Thursday, 17 December, 2015 7:24 AM
To: rietveld_l@ill.fr
Subject: Re: structure solution terminology

I agree with Yaroslav Filinchuk's thoughts:

"However, the "structure solution in direct space" does not attempt to work in 
the reciprocal space - all the manipulations are done in the direct space."

RMC, normal MC, genetic algorithms, they all shuffle electron density in some 
or another way in real space. So 'real space structure solution' 
sounds the best, and 'real space' is better than 'direct space' as to avoid 
confusion with 'direct methods'.

Arie
ps: we should propose a new possible data value for 
_atom_sites_solution_primary By the way the data value vecmap (real-space 
vector search) is, I suppose, equivalent to a real-space Patterson search, 
which is indeed not the same as  RMC, normal MC, genetic algorithms or other 
shuffle methods.


Mike Glazer wrote the following on 17/12/2015 12:50:
> But the original question was:
> What's the right nickname for the method of structure solution from powders, 
> which instead of analyzing electron (nuclear) density shuffles atoms or 
> molecules around a cell and compares experimental and calculated patterns ?
> That's what we do with RMC in practice. We use RMC to create models and then 
> compare with experimental patterns.
> Mike
>
> Professor A M Glazer
> Department of Physics
> Parks Road
> Oxford
> OX1 3PU
> United Kingdom
> Tel/Fax: 44 1865 272290
> Mobile: 0778 696 0537
> **
> Vice-President of the International Union of Crystallography Emeritus 
> Professor of Physics and Emeritus  Fellow of Jesus College Oxford 
> Visiting Professor at the University of Warwick Crystallographer
> **
> " Je ne te parlerai que cristaux" L. Pasteur (1850)
>
>
> http://ukcatalogue.oup.com/product/9780198744306.do
>
>
> -Original Message-
> From: Radovan Cerny [mailto:radovan.ce...@unige.ch]
> Sent: 17 December 2015 11:03
> To: Mike Glazer ; Lubomir Smrcok 
> ; Leonid Solovyov 
> Cc: rietveld_l@ill.fr
> Subject: RE: structure solution terminology
>
> RMC covers only a part of the "Direct space methods", not for example methods 
> using evolution algorithms.
>
>
> Radovan Cerny
> Laboratoire de Cristallographie, DQMP
> Université de Genève
> 24, quai Ernest-Ansermet
> CH-1211 Geneva 4, Switzerland
> Phone  : [+[41] 22] 37 964 50, FAX : [+[41] 22] 37 961 08 mailto : 
> radovan.ce...@unige.ch
> URL: http://www.unige.ch/sciences/crystal/cerny/rcerny.htm
>
>
> -Message d'origine-
> De : rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] De la part 
> de Mike Glazer Envoyé : jeudi 17 décembre 2015 11:49 À : Lubomir Smrcok; 
> Leonid Solovyov Cc : rietveld_l@ill.fr Objet : RE: structure solution 
> terminology
>
> This all sounds like Reverse MonteCarlo (RMC) modelling. We have used this 
> with PDF analysis.
> Mike Glazer
>
>
>
> ++
> Please do NOT attach files to the whole list 
> Send commands to  eg: HELP as the subject with no body text
> The Rietveld_L list archive is on 
> http://www.mail-archive.com/rietveld_l@ill.fr/
> ++
>


-- 
**
A. van der Lee
Institut Européen des Membranes
CNRS - UMR 5635
Université de Montpellier II - Case Courrier 047
Place E. Bataillon
34095 MONTPELLIER Cedex 5 - FRANCE

Tel : 33 (0) 4 67 14 91 35
Fax : 33 (0) 4 67 14 91 19

**
member of RECIPROCS - Réseau des Enseignants, Chercheurs et ITA
Professionnels de la Cristallographie Structurale (French professional
crystallographer network):
http://metiersit.dsi.cnrs.fr/index.php?page=ReseauMetiers&codeBap=B
**
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Send commands to  eg: HELP as the subject with no body text
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++

Re: structure solution terminology

[A. van der Lee]

I agree with Yaroslav Filinchuk's thoughts:

"However, the "structure solution in direct space" does not attempt to
work in the reciprocal space - all the manipulations are done in the
direct space."

RMC, normal MC, genetic algorithms, they all shuffle electron density in 
some or another way in real space. So 'real space structure solution' 
sounds the best, and 'real space' is better than 'direct space' as to 
avoid confusion with 'direct methods'.


Arie
ps: we should propose a new possible data value for 
_atom_sites_solution_primary
By the way the data value vecmap (real-space vector search) is, I 
suppose, equivalent to a real-space Patterson search, which is indeed 
not the same as  RMC, normal MC, genetic algorithms or other shuffle 
methods.



Mike Glazer wrote the following on 17/12/2015 12:50:

But the original question was:
What's the right nickname for the method of structure solution from powders, 
which instead of analyzing electron (nuclear) density shuffles atoms or 
molecules around a cell and compares experimental and calculated patterns ?
That's what we do with RMC in practice. We use RMC to create models and then 
compare with experimental patterns.
Mike

Professor A M Glazer
Department of Physics
Parks Road
Oxford
OX1 3PU
United Kingdom
Tel/Fax: 44 1865 272290
Mobile: 0778 696 0537
**
Vice-President of the International Union of Crystallography
Emeritus Professor of Physics and
Emeritus  Fellow of Jesus College Oxford
Visiting Professor at the University of Warwick
Crystallographer
**
" Je ne te parlerai que cristaux" L. Pasteur (1850)


http://ukcatalogue.oup.com/product/9780198744306.do


-Original Message-
From: Radovan Cerny [mailto:radovan.ce...@unige.ch]
Sent: 17 December 2015 11:03
To: Mike Glazer ; Lubomir Smrcok ; 
Leonid Solovyov 
Cc: rietveld_l@ill.fr
Subject: RE: structure solution terminology

RMC covers only a part of the "Direct space methods", not for example methods 
using evolution algorithms.


Radovan Cerny
Laboratoire de Cristallographie, DQMP
Université de Genève
24, quai Ernest-Ansermet
CH-1211 Geneva 4, Switzerland
Phone  : [+[41] 22] 37 964 50, FAX : [+[41] 22] 37 961 08 mailto : 
radovan.ce...@unige.ch
URL: http://www.unige.ch/sciences/crystal/cerny/rcerny.htm


-Message d'origine-
De : rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] De la part de 
Mike Glazer Envoyé : jeudi 17 décembre 2015 11:49 À : Lubomir Smrcok; Leonid 
Solovyov Cc : rietveld_l@ill.fr Objet : RE: structure solution terminology

This all sounds like Reverse MonteCarlo (RMC) modelling. We have used this with 
PDF analysis.
Mike Glazer



++
Please do NOT attach files to the whole list 
Send commands to  eg: HELP as the subject with no body text
The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/
++




--
**
A. van der Lee
Institut Européen des Membranes
CNRS - UMR 5635
Université de Montpellier II - Case Courrier 047
Place E. Bataillon
34095 MONTPELLIER Cedex 5 - FRANCE

Tel : 33 (0) 4 67 14 91 35
Fax : 33 (0) 4 67 14 91 19

**
member of RECIPROCS - Réseau des Enseignants, Chercheurs et ITA
Professionnels de la Cristallographie Structurale (French professional
crystallographer network):
http://metiersit.dsi.cnrs.fr/index.php?page=ReseauMetiers&codeBap=B
**
++
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++

RE: structure solution terminology

[Mike Glazer]

But the original question was:
What's the right nickname for the method of structure solution from powders, 
which instead of analyzing electron (nuclear) density shuffles atoms or 
molecules around a cell and compares experimental and calculated patterns ?
That's what we do with RMC in practice. We use RMC to create models and then 
compare with experimental patterns.
Mike

Professor A M Glazer
Department of Physics
Parks Road
Oxford
OX1 3PU
United Kingdom
Tel/Fax: 44 1865 272290
Mobile: 0778 696 0537
**
Vice-President of the International Union of Crystallography
Emeritus Professor of Physics and
Emeritus  Fellow of Jesus College Oxford
Visiting Professor at the University of Warwick
Crystallographer
**
" Je ne te parlerai que cristaux" L. Pasteur (1850) 


http://ukcatalogue.oup.com/product/9780198744306.do


-Original Message-
From: Radovan Cerny [mailto:radovan.ce...@unige.ch] 
Sent: 17 December 2015 11:03
To: Mike Glazer ; Lubomir Smrcok 
; Leonid Solovyov 
Cc: rietveld_l@ill.fr
Subject: RE: structure solution terminology

RMC covers only a part of the "Direct space methods", not for example methods 
using evolution algorithms.


Radovan Cerny  
Laboratoire de Cristallographie, DQMP
Université de Genève
24, quai Ernest-Ansermet  
CH-1211 Geneva 4, Switzerland
Phone  : [+[41] 22] 37 964 50, FAX : [+[41] 22] 37 961 08 mailto : 
radovan.ce...@unige.ch
URL: http://www.unige.ch/sciences/crystal/cerny/rcerny.htm


-Message d'origine-
De : rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] De la part de 
Mike Glazer Envoyé : jeudi 17 décembre 2015 11:49 À : Lubomir Smrcok; Leonid 
Solovyov Cc : rietveld_l@ill.fr Objet : RE: structure solution terminology

This all sounds like Reverse MonteCarlo (RMC) modelling. We have used this with 
PDF analysis. 
Mike Glazer

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RE: structure solution terminology

[Radovan Cerny]

RMC covers only a part of the "Direct space methods", not for example methods 
using evolution algorithms.


Radovan Cerny  
Laboratoire de Cristallographie, DQMP
Université de Genève
24, quai Ernest-Ansermet  
CH-1211 Geneva 4, Switzerland
Phone  : [+[41] 22] 37 964 50, FAX : [+[41] 22] 37 961 08
mailto : radovan.ce...@unige.ch
URL: http://www.unige.ch/sciences/crystal/cerny/rcerny.htm


-Message d'origine-
De : rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] De la part de 
Mike Glazer
Envoyé : jeudi 17 décembre 2015 11:49
À : Lubomir Smrcok; Leonid Solovyov
Cc : rietveld_l@ill.fr
Objet : RE: structure solution terminology

This all sounds like Reverse MonteCarlo (RMC) modelling. We have used this with 
PDF analysis. 
Mike Glazer

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RE: structure solution terminology

[Mike Glazer]

This all sounds like Reverse MonteCarlo (RMC) modelling. We have used this with 
PDF analysis. 
Mike Glazer

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RE: structure solution terminology

[Radovan Cerny]

IUCr. itself is not always coherent. Sometime the dictionary speaks about "real 
space" (see the link which Arie has posted: 
http://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_sites_solution_primary.html),
 sometimes about "direct space" (your link: 
http://reference.iucr.org/dictionary/Direct_space).


I have tried to introduce new terminology (to left some heritage after myself 
...):

Intensity extraction based methods (ab initio methods): That's what you need, 
the Bragg intensities, and then you can do what you want with them (direct 
methods, Patterson, charge flipping ...)

Pattern modelling (model dependent methods): And you choose any algorithm, 
method to model your pattern.


Both have their observations in reciprocal space, and we do not need to discus 
where your method is working. In any space, in both, wherever you like.

I hope that Lubo will be one day satisfied, and can continue writing his paper 
after the difficult Introduction.

Radovan

Radovan Cerny  
Laboratoire de Cristallographie, DQMP
Université de Genève
24, quai Ernest-Ansermet  
CH-1211 Geneva 4, Switzerland
Phone  : [+[41] 22] 37 964 50, FAX : [+[41] 22] 37 961 08
mailto : radovan.ce...@unige.ch
URL: http://www.unige.ch/sciences/crystal/cerny/rcerny.htm


-Message d'origine-
De : rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] De la part de 
Jonathan WRIGHT
Envoyé : jeudi 17 décembre 2015 09:28
À : rietveld_l@ill.fr
Objet : Re: structure solution terminology

On 16/12/2015 23:05, Lubomir Smrcok wrote:
>  shuffles atoms or molecules around
> a cell and compares experimental and calculated patterns ? It could be 
> well used also for single crystal data, I know, but it is not 
> routinely done (yet ?).

In protein crystallography one says "molecular replacement" and this is 
routinely done. For small molecule single crystal data, perhaps the phrase is 
"dirdif" ? In both of those cases the matching is in a real-space Patterson 
function, which is effectively comparing patterns.

Direct space is defined here :
http://reference.iucr.org/dictionary/Direct_space
... so when someone says "structure solution in direct space" it seems fairly 
clear and surely sounds better than "structure solution by intelligent 
guesswork" :-)

Best,

Jon


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Re: structure solution terminology

[Johannes Birkenstock]

Dear Lubomir,

I' afraid that I might not get exactly what you mean. Are you talking 
about something you actually use or are you looking for a term on a 
method that exists somewhere "out there" and that you would like to use 
potentially?


Assuming the latter, the closest I could think of is not really a 
structure solution method but rather a structure completion method - and 
this one is called "grid search method". It was introduced by Baur and 
Fischer (1986). We apply it to incomplete structure models in a Rietveld 
program: we are shifting a dummy atom (of a selected element) 
systematically through the unit cell (i.e., it is a direct space 
method), at each new fixed position (x,y,z) we refine its SOF and the 
phases's scale and calculate the R-values while fixing all other 
parameters. Then two maps are created, one with R as function of (x,y,z) 
and one with SOF(x,y,z). The best position (x,y,z) (if any) of the atom 
shows up as the absolute maximum (or several equivalent maxima for 
equivalent positions) in the SOF map while the R-map shows an absolute 
minimum (or several equivalent ones) at the same (x,y,z) as for the 
SOF-maximum. Clearly, the systematic grid search may be confined to any 
subsection of the unit cell. Different from Fourier methods the grid 
search method does not suffer from termination effects, however, it is 
rather time consuming...


Sorry if this should not match what you are looking for, as it is for 
structure completion only and it definitely would not work for structure 
solution from scratch. Anyway, here is the original citation:


Baur, W.H. and Fischer, R.X. (1986) Recognition and treatment of 
background problems  in  neutron  powder  diffraction  refinements. In  
C.S.  Barrett,  J.B. Cohen, J. Faber, R. Jenkins, D.E. Leyden, J.C. 
Russ, and P.K. Predecki, Eds., Advances in X-ray Analysis, 29, p. 
131–142. Plenum Publishing Corporation, New York.


Best regards,
Johannes


Am 17.12.2015 um 07:54 schrieb Lubomir Smrcok:

OK,
But I am sure that any deciphering is a systematic rather than a 
random process. I can however agree that when such a systematic 
process is fueled by drinks, some random mental leaps might play a role.
This fact, unfortunately, does not help in solving this terminology 
problem - at least not here.

Regards,
Lubo


On Thu, 17 Dec 2015, Leonid Solovyov wrote:

What's the right nickname for the method of structure solution from 
powders


In Russian we use an equivalent to 'structure decipher'.
Sometimes, however, this is really 'structure solution' when we apply 
vodka in the process ;)


***
Leonid A. Solovyov
Institute of Chemistry and Chemical Technology
660036, Akademgorodok 50/24, Krasnoyarsk, Russia
http://sites.google.com/site/solovyovleonid
***


On Thu, 12/17/15, Lubomir Smrcok  wrote:

Subject: structure solution terminology
To: rietveld_l@ill.fr
Date: Thursday, December 17, 2015, 5:05 AM

Hi,

I feel I have a problem with terminology. What's the right
nickname for
the method of structure solution from powders, which instead
of analyzing
electron (nuclear) density shuffles atoms or molecules
around a cell and
compares experimental and calculated patterns ? It could be
well used also
for single crystal data, I know, but it is not routinely
done (yet ?).

I remember that colloquially used phrase "structure solution
in direct
space" woke me up several times during plenary lectures at
several
conferences. What are we having in direct space ? IMHO just
electron
(nuclear) density. Its FT is our diffractogram so that if we
fit
diffractogram, are we still in direct space ? Of course,
reciprocal space
is a pure math and diffracted beam is quite realistic (BTW,
are
there photons also in reciprocal space :-) ?). But in which
space are we when doing any
crystallographic calculation ? OK, OK, you know what I am
asking ... no
bad jokes, please.

May I ask for your 2 cents ?
Thanks,
Lubo




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--
Dr. Johannes Birkenstock
Univ. Bremen
FB5-Geow., Kristallographie/ ZEKAM
GEO, R2300
Klagenfurter Strasse 2
D-28359 Bremen
Tel. ++49 (0)421 218-65165
FAX. ++49 (0)421 218-65189
www.zekam.uni-bremen.de

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Re: structure solution terminology

[Lubomir Smrcok]

Perfect ! But fancy a sentence in your future paper : Crystal structure 
was solved by other method. 
lubo


On Thu, 17 Dec 2015, A. van der Lee wrote:


According to the IUCr it should be named 'other'.
See here:

cif tag 'atom_sites_solution_primary'


best wishes, Arie




On Thu, 17 Dec 2015, Leonid Solovyov wrote:


What's the right nickname for the method of structure solution from
powders


In Russian we use an equivalent to 'structure decipher'.
Sometimes, however, this is really 'structure solution' when we apply
vodka in the process ;)

***
Leonid A. Solovyov
Institute of Chemistry and Chemical Technology
660036, Akademgorodok 50/24, Krasnoyarsk, Russia
http://sites.google.com/site/solovyovleonid
***


On Thu, 12/17/15, Lubomir Smrcok  wrote:

Subject: structure solution terminology
To: rietveld_l@ill.fr
Date: Thursday, December 17, 2015, 5:05 AM

Hi,

I feel I have a problem with terminology. What's the right
nickname for
the method of structure solution from powders, which instead
of analyzing
electron (nuclear) density shuffles atoms or molecules
around a cell and
compares experimental and calculated patterns ? It could be
well used also
for single crystal data, I know, but it is not routinely
done (yet ?).

I remember that colloquially used phrase "structure solution
in direct
space" woke me up several times during plenary lectures at
several
conferences. What are we having in direct space ? IMHO just
electron
(nuclear) density. Its FT is our diffractogram so that if we
fit
diffractogram, are we still in direct space ? Of course,
reciprocal space
is a pure math and diffracted beam is quite realistic (BTW,
are
there photons also in reciprocal space :-) ?). But in which
space are we when doing any
crystallographic calculation ? OK, OK, you know what I am
asking ... no
bad jokes, please.

May I ask for your 2 cents ?
Thanks,
Lubo




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++




--
**
A. van der Lee
Institut Européen des Membranes
CNRS - UMR 5635
Université de Montpellier II - Case Courrier 047
Place E. Bataillon
34095 MONTPELLIER Cedex 5 - FRANCE

Tel : 33 (0) 4 67 14 91 35
Fax : 33 (0) 4 67 14 91 19

**
member of RECIPROCS - Réseau des Enseignants, Chercheurs et ITA
Professionnels de la Cristallographie Structurale (French professional
crystallographer network):
http://metiersit.dsi.cnrs.fr/index.php?page=ReseauMetiers&codeBap=B
**
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Re: structure solution terminology

[Jonathan WRIGHT]

On 16/12/2015 23:05, Lubomir Smrcok wrote:

 shuffles atoms or molecules around
a cell and compares experimental and calculated patterns ? It could be
well used also for single crystal data, I know, but it is not routinely
done (yet ?).


In protein crystallography one says "molecular replacement" and this is 
routinely done. For small molecule single crystal data, perhaps the 
phrase is "dirdif" ? In both of those cases the matching is in a 
real-space Patterson function, which is effectively comparing patterns.


Direct space is defined here :
http://reference.iucr.org/dictionary/Direct_space
... so when someone says "structure solution in direct space" it seems 
fairly clear and surely sounds better than "structure solution by 
intelligent guesswork" :-)


Best,

Jon


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Re: structure solution terminology

[A. van der Lee]

According to the IUCr it should be named 'other'.
See here:

cif tag 'atom_sites_solution_primary'


best wishes, Arie




On Thu, 17 Dec 2015, Leonid Solovyov wrote:


What's the right nickname for the method of structure solution from
powders


In Russian we use an equivalent to 'structure decipher'.
Sometimes, however, this is really 'structure solution' when we apply
vodka in the process ;)

***
Leonid A. Solovyov
Institute of Chemistry and Chemical Technology
660036, Akademgorodok 50/24, Krasnoyarsk, Russia
http://sites.google.com/site/solovyovleonid
***


On Thu, 12/17/15, Lubomir Smrcok  wrote:

Subject: structure solution terminology
To: rietveld_l@ill.fr
Date: Thursday, December 17, 2015, 5:05 AM

Hi,

I feel I have a problem with terminology. What's the right
nickname for
the method of structure solution from powders, which instead
of analyzing
electron (nuclear) density shuffles atoms or molecules
around a cell and
compares experimental and calculated patterns ? It could be
well used also
for single crystal data, I know, but it is not routinely
done (yet ?).

I remember that colloquially used phrase "structure solution
in direct
space" woke me up several times during plenary lectures at
several
conferences. What are we having in direct space ? IMHO just
electron
(nuclear) density. Its FT is our diffractogram so that if we
fit
diffractogram, are we still in direct space ? Of course,
reciprocal space
is a pure math and diffracted beam is quite realistic (BTW,
are
there photons also in reciprocal space :-) ?). But in which
space are we when doing any
crystallographic calculation ? OK, OK, you know what I am
asking ... no
bad jokes, please.

May I ask for your 2 cents ?
Thanks,
Lubo




++
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--
**
A. van der Lee
Institut Européen des Membranes
CNRS - UMR 5635
Université de Montpellier II - Case Courrier 047
Place E. Bataillon
34095 MONTPELLIER Cedex 5 - FRANCE

Tel : 33 (0) 4 67 14 91 35
Fax : 33 (0) 4 67 14 91 19

**
member of RECIPROCS - Réseau des Enseignants, Chercheurs et ITA
Professionnels de la Cristallographie Structurale (French professional
crystallographer network):
http://metiersit.dsi.cnrs.fr/index.php?page=ReseauMetiers&codeBap=B
**
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