[Ifeffit] Autobk parameters

[Stefano Ciurli]

Bruce,

>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!

thanks for not making me feel like I am bugging you all the times... 
:-)) and for the time spent here for us

>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.

we did not do that... and I have never seen it done for biological 
samples in the short experience I have had. So I hope it is really 
not too essential as long as the fitted E0 are not too different from 
the zero-valent atom (few eV, right?)

>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.

OK

>  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.

OK. Good.

>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.

I think I understand that I should use one of the .DAT files produced 
by feff as a standard to optimize the short R range (less than Rbgk), 
right? well, I tried to do that. First of all the purpose of my study 
is to sort out the number and type of ligands to the Ni and Zn in our 
protein, so we do not know that. I could in principle use a .DAT file 
coming from, let's say, Ni(H2O)62+ (nickel hexa-aquo ion), whose 
structure I could get from a crystallographic database or from a 
q-chem calculation. Of course in that case I will only have a single 
shell, but that may be enough? What if I use NONE as a standard? In 
that case the pre-first-shell peak is not removed very well at all... 
but I know that it is not that important for the fitting, as for that 
I will start fitting at higher R... right?

>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

I have gone through that. I am able to do it by now :-)) tnx!

>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.

OK

>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.

nickel or zinc hexa-aquo is enough then?

>  > 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.

OK!

>  > 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.

OK, now I get it.

>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.

OK. If the following criterium is wrong - as I understand - then the 
guessed values by the program are actually very good.

>  > 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.
>

Who knows where I found that idea? I am certain I have read it somewhere...

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

Being on a different time, I am done for today and going to pick up 
my kids from school. I look forward to reading more of your wisdom 
(and others as well, if willing) later on tonight or tomorrow.
Ciao,
Stefano
-- 
____________________________________________

Stefano Ciurli
Professor of Chemistry
Department of Agro-Environmental Science and Technology
University of Bologna
Viale Giuseppe Fanin, 40
I-40127 Bologna
Italy
Phone:	+39-051-209-6204
Fax:	+39-051-209-6203

"Fatti non foste a viver come bruti,
ma per seguir virtute e canoscenza"
Dante Alighieri - Inferno - Canto XXVI