[Ifeffit] Other programs than FEFF - GNXAS and MXAN

Matthew MAMarcus at lbl.gov
Sun Jul 30 16:27:42 CDT 2006

What I like to say is that EXAFS works best when you already know most
of the answer.  I thought it was so well-known as to need no repeating that
putting a completely unknown sample in the beam is futile unless you happen
to liuck onto finding an EXAFS spectrum you recognize.
----- Original Message ----- 
From: "Sven L.M. Schroeder" <s.schroeder at manchester.ac.uk>
To: "'XAFS Analysis using Ifeffit'" <ifeffit at millenia.cars.aps.anl.gov>
Sent: Sunday, July 30, 2006 1:21 PM
Subject: RE: [Ifeffit] Other programs than FEFF - GNXAS and MXAN

> 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.
> 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
> done through the human operator.
> The conceptual challenge for the design of any 'XAFS black box' is to find
> 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,
> 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
> can almost always get 'for free' with any EXAFS measurement. There is
> 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
> least).
> --
> 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
> M60 1QD United Kingdom
> http://www.slmslab.info
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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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