[Ifeffit] Other programs than FEFF - GNXAS and MXAN
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...
Sarah Lawrence College
>Ah! The "black box" discussion. That's a fun way to waste lots of
>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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