[Ifeffit] Other programs than FEFF - GNXAS and MXAN

Scott Calvin SCalvin at slc.edu
Sun Jul 30 07:20:58 CDT 2006

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
>Well, that was my US$0.02 worth...

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