[Ifeffit] Other programs than FEFF - GNXAS and MXAN

Sven L.M. Schroeder s.schroeder at manchester.ac.uk
Sun Jul 30 15:21:10 CDT 2006

Let me add my 2 *pence* worth, as the Manchester team was mentioned too.

I agree with Calvin that a true 'ab initio' EXAFS black-box for a sample
about which nothing else is known is probably a non-sensical proposition. As
with so many other (any other?) technique that probes molecular level
properties one needs additional information about the sample, or more
gerenally, 'prior knowledge'. Now, with XAFS we have a technique that is
really only let loose on samples (if not the experimentalist then the
beamtime committees will usually see to that...) that have already been
characterised to quite some level of detail. Even during in situ
measurements on dynamic systems (reactions, phase transitions, in vivo,
etc), where the nature of the sample is more open-ended, the possibilities
are quite restricted. But the range of possible elements in the sample is
practically always limited (at least within the concentration ranges that
can be probed by XAFS), there are also rules about reasonable ranges for
bond lengths out there, phase diagrams, etc. All of these constrain the
possible parameter space quite significantly - and that is what is currently
done through the human operator.

The conceptual challenge for the design of any 'XAFS black box' is to find a
way to integrate this prior knowledge into the analysis process. I, as a
physical chemist, sometimes call the challenge 'How to teach a computer
chemical intuition'. Bond length rules, or more generally, any knowledge
from inorganic chemistry textbooks - there is no principal reason why all
this could not be coded into a database for a decision-making system, which
would then have to be coupled to a generic EXAFS analysis interface that
allows people to constrain a search according to what they already know
about their samples. A Herculean job before it becomes elegant...

Also, let's not forget the XANES. In principle that is information that you
can almost always get 'for free' with any EXAFS measurement. There is really
a lot of information to be mined through proper XANES analysis - but we
still have a lot of work to do to get there ... 

Good news I guess. Keeps us busy for some years to come!

So that makes roughly 8 cents now (1p = 2c, approximately, at the moment at

Sven L.M. Schroeder (mailto:s.schroeder at manchester.ac.uk)

School of Chemical Engineering and Analytical Science (CEAS) & School of
Chemistry The University of Manchester PO Box 88 Sackville Street Manchester
M60 1QD United Kingdom


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> -----Original Message-----
> From: ifeffit-bounces at millenia.cars.aps.anl.gov 
> [mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf 
> Of Scott Calvin
> Sent: 30 July 2006 07:21
> To: XAFS Analysis using Ifeffit
> Subject: Re: [Ifeffit] Other programs than FEFF - GNXAS and MXAN
> Well, I have some time to waste, and since my name was just 
> mentioned...
> I think a black box is a wonderful idea for cases where the 
> space of possible solutions is very limited. At the same 
> conference that the UK group presented, Wolfram Meyer-Klaucke 
> gave a very nice talk on a black-box system for determining 
> protein structure around an active site. The talk was 
> opposite the UK group's, so unfortunately no one saw both.
> In any case, that's a perfect situation for automation: there 
> are a very limited number of ligands that could be present, 
> and their structures are very well understood. It's much more 
> than fingerprinting, since the combination of ligands might 
> never have seen before. Their system even allows for the 
> ligands to be at slightly unusual distances. But it only 
> works because the biochemistry is already pretty well 
> understood and quite limited. 
> Although a very different system, I suspect the UK automation 
> of supported metal catalysts has similarly limited scope; 
> neither system would probably work very well when fed data 
> meant for the other!
> I think there's sometimes a wish for a system that acts like 
> a Star Trek tricorder: stick any spectrum in, and the 
> computer can say "it appears to be an oxide with coordination 
> number 6." In my opinion, that kind of system will never be 
> developed, because there just isn't that much information 
> sitting in the EXAFS. (Some of you new to EXAFS may be 
> puzzled by that--it doesn't sound like very much information 
> at all. But if you're going to allow me the space of all 
> possible structures along with less-than-perfect data, it's 
> hard to distinguish disorder from coordination number 
> changes, for example, and it's in turn hard to distinguish 
> true disorder from splitting below the resolution of the data.)
> In other words, current experts in EXAFS analysis don't act 
> as black boxes to the outside world. If 
> <pick-your-favorite-expert> were brought a spectrum and asked 
> "OK, tell me the structure," the expert would immediately 
> start asking questions to gain additional information (or 
> would say "no," and walk off in a huff). If experts don't act 
> as black boxes, then neither can a computer.
> OK, with my two cents added to Bruce, that now makes four...
> --Scott Calvin
> Sarah Lawrence College
> >Ah!  The "black box" discussion.  That's a fun way to waste lots of 
> >time. ;-)
> >
> >The physics has its complicated parts, but I suspect that we have a 
> >sufficient understanding of the problems.  There are many 
> applications 
> >where a black box is reasonable to consider and probably would even 
> >work pretty well.  At the recent XAFS conference, the group from 
> >Manchester, UK presented a high-throughput scheme that involves 
> >automate processing of larfge quantities of data.  They seem to get 
> >good results with minimal human intervention.  And Harald 
> Funke gave a 
> >really neat talk about Feff-based wavelets that could be a 
> very useful 
> >approach to a first-shell black-box.
> >
> >There will always be a large part of exafs analysis that falls well 
> >outside the scope the black box.  The sorts of crazy fits 
> published by 
> >some of the frequent contributors to this list (I am thinking 
> >specifically of Scott Calvin and Shelly Kelly) will always defy 
> >automation.
> >
> >Well, that was my US$0.02 worth...
> >B
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