[Ifeffit] Autobk parameters

[Bruce Ravel]

Stefano,

What an excellent email!  These are very insightful questions that
will, I presume, prompt all sorts of good discussion.  What a great
use of the mailing list!

I am going to answer a few of the questions in this email, but leave
others for later or for others to take a stab at.

> 1) I understand that energy calibration should be performed, and I
> did so by using the atomic edge energy. I also understand that this
> parameter could be fluctuating in the subsequent fitting. Any comment
> on this procedure?

Often energy calibration is made using a reference spectrum (in your
case an Ni or Fe foil) measures simultaneously (or perhaps right
before or right after) with the sample.  That way you can measure an
energy shift relative to the 0 valent metal.

Also you should be aware that, although Feff's relative energy scale
is accurate, it's absolute energy scale may not be.  Consquently, one
almost always needs an e0 parameter when fitting using Feff in order
to "line up" the energy grids of the data and the theory.  This is not
to say that energy calibration is pointless.  Quite the contrary.
Along with the energy shifts I mentioned above, you want all of your
data to be align and calibrated so that the e0's you measure when
fitting are internally consistent within the data ensemble.

> 3) I understood from the paper by Matt (and from the "Using Athena"
> manual by Bruce) that one could use a "standard" to estimate the
> level of leakage into the small chi(R) region (apodization effects
> due to Fourier window filtering). The manual states that one can read
> in a chi.dat file produced with feff. However, I do not understand
> how to build the feff.inp for feff and produce a useful chi.dat to
> use as a "standard". Please help?

Since you are looking at proteins, I'll give the "protein answer"
rather than the "crystal answer".  You will need a protein data bank
file for your protein or for something that you think is similar.

A simple example of converting a PDB file to a feff.inp file is shown
on page 2.5 ("Preparing the FEFF input file for non-crystalline
materials") of this document:
  http://cars9.uchicago.edu/xafs/NSLS_EDCA/Sept2002/Ravel.pdf

Note that Feff does NOT require that the central atom is at (0,0,0).
Also Feff does NOT require that the atoms list be in any particular
order.  Thus, you can take just the bit around your metal atom from
the PDB file and doctor it up as explained on that page.

If there is no PDB file for your exact protein, pick something
similar.  As long as its close, that should be enough to begin
interpreting the data.

> 5) The Pre-edge range: here the manual (and the online help) states
> that the range is -200 to - <snip> (btw, is there a way to see the
> end of the long sentences in the echo area?) but the actual default

Go to the Edit menu and select "Echo buffer".  The complete sentence
is written there.

The sentences are being snipped because sentences that are too long
make the whole window expand to show them.  That is kind of jarring
and confusing.  As I've been using Athena and finding examples of
lines that are too long, I have been editing them to be shorter.

> values are -150/-75 for most cases, while it can be different for
> different spectra. I do not understand the rationale in choosing
> these default values. I am guessing that the program somehow finds
> the "best" range and uses it. If so, i would like to know the
> criteria for this choice. 

The defaults are indeed -200 to -30, but the first value will be reset
if it is lower then the first data point.  You can set values that you
think are appropriate in the preferences dialog.  The rationale for
this choice is that, umm... well... ummm....., they are pretty
reasonable guesses for most data sets and when they are not reasonable
guesses then you can change them.  Not much of a reason, but I don't
know what else to say.

> Also, I read somewhere in your documents
> that one should try to have the pre-edge and the post-edge lines to
> run parallel. Is this a good criterium? Should I change the pre- and
> post-edge ranges in order to satisfy this criterium? If the default
> values yield non-parallel lines should I worry? If so, what should I
> do?

My, my!  Certainly not.  Not only are they not parallel by the physics
of the absorption processes, they are usually more non-parallel in
practice due to detector and sample effects.  The pre and post edge
lines should go through the data.  *That* is the only good rule.



OK, I'm going to go get a cup of coffee now.  I'll poke at these
questions some more later on.

B


-- 
 Bruce Ravel  ----------------------------------- ravel at phys.washington.edu
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 Naval Research Laboratory                          phone: (1) 202 767 2268
 Washington DC 20375, USA                             fax: (1) 202 767 4642

 NRL Synchrotron Radiation Consortium (NRL-SRC)
 Beamlines X11a, X11b, X23b
 National Synchrotron Light Source
 Brookhaven National Laboratory, Upton, NY 11973

 My homepage:    http://feff.phys.washington.edu/~ravel 
 EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/