[Ifeffit] graphics and fit

[Jeff Terry]

Hi Shelly,

That would be a great program to have.
I often have to do this.
I hope that you make the program available.



Jeff


On May 13, 2004, at 10:13 AM, Kelly, Shelly D. wrote:

>
> 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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>
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