[Ifeffit] graphics and fit

[Carlo U. Segre]

rasmol and xmakemol also can read "*.xyz" files as well as many other
formats.  These programs are more suited to macromolecular structures.

Carlo


On Thu, 13 May 2004, Kelly, Shelly D. wrote:

> 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
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit at millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit
> >
>
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-- 
Carlo U. Segre -- Professor of Physics
Associate Dean for Special Projects, Graduate College
Illinois Institute of Technology
Voice: 312.567.3498            Fax: 312.567.3494
segre at agni.phys.iit.edu    http://www.iit.edu/~segre