[Ifeffit] graphics and fit

[Kelly, Shelly D.]

Hi Stefano,

Another free program that can read the output from atoms is ghemical.
http://www.uku.fi/~thassine/ghemical/

I have written a rather specialized code that allows you to rotate a
group of atoms until one of those atoms is at a determined distance from
the original atom.  Here let me explain for the specific example that I
used it for.  Say you have a Uranium atom and attached to it through an
oxygen atom you have a PO4 group.  One of the oxygen atoms of the PO4
group is shared with the uranium atom.  Now from your exafs data you
know that the U-P distance should be some number call it Rp.  This
program will leave the shared oxygen atom at the same spot, but move the
PO3 atoms until the distance for U-P matches Rp.  There are lots of ways
that you can move the PO3 atom.  The program is written to try to bend
the PO3 group first and then translate the PO3 group to make the
distance match.  Then the program writes out the coordinates for all the
atoms.  This code is written in perl and doesn't have a gui interface,
but I would be happy to share.



Shelly
> -----Original Message-----
> From: Stefano Ciurli [mailto:stefano.ciurli at unibo.it] 
> Sent: Thursday, May 13, 2004 5:31 AM
> To: XAFS Analysis using Ifeffit
> Subject: [Ifeffit] graphics and fit
> 
> 
> Hello,
> 
> just a thought: wouldn't it be nice to be able to read the feff.inp 
> file directly into a simple molecular graphics program in order to 
> see if the used coordinates contain any error? Maybe it is possible 
> already and I am not aware of it. I understand that the program is 
> mainly used by material scientists, but for us working with 
> biological samples of metalloproteins it would be nice.
> Another suggestion: I know that Excurve is able to treat the 
> histidine rings as a unity, and when performing the fit that program 
> is able to maintain the ring rigid while fitting the distance between 
> the metal and the imidazole ring of the histidine. How can I do that 
> simply using your suite?
> 
> 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 
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