[Ifeffit] graphics and fit

[Paul Fons]

I guess I should elaborate a little -- you can generate a feff.inp file 
using atoms within artemis and and save the output in another format as 
well (there are several different options including pdb).  The common 
source would be the atoms.inp file then if you had saved the data 
beforehand or manually entered information for a new atoms page.

If you want to take a feff.inp file and change it to a pdb, you will 
need to do this yourself. I wrote a perl script to do it (I can see if 
it is on my laptop tomorrow).  I am hardly the Perl master that Bruce 
is though, perhaps he (or someone else on the list) has written a perl 
script to make a pdb file from a feff input file (it is just a matter 
of rearranging and adding additional columns of information).  The 
hardest part, the coordinates are already there.


						Paul


On May 18, 2004, at 10:22 PM, Stefano Ciurli wrote:

> Dear Paul,
> thanks for your message.
>
>> As I happen to be in Italy (at Elettra) at the moment and am on the 
>> same time, I thought I would reply.  Have you tried using the artemis 
>> module for reading in the feff.inp file.
>
> yes. I am able to do it and able to run fits with Artemis no problem. 
> I did not realize that Artemis could export feff.inp files to pdb. I 
> tried to: after reading in a feff.inp file, I follow FEFF -> write 
> special output -> pdb, but I get the error message "You did not 
> specify any lattice constant" which of course it is not necessary 
> neither for a feff.inp file nor for a pdb file. So I am stuck.
>
>>  I have done this many times and successfully exported the pdb file. 
>> For viewing the pdb file I used to use vmd (from the University of 
>> Illinois -- a free program and capable of ray-tracing and atom 
>> selection by type, distance etc.), but now I am using crystalmaker 
>> which does more in the crystallography front.
>
> I have VMD installed on my Mac, as well as DeepView, Rasmol, MolMol, 
> iMol, PyMol, O, and Chimera... The problem is not visualizing a PDB 
> file... but rather to export the feff.inp file into a pdb and see what 
> I am actually using, coordinate-wise.
>
> Any chance to pass by Bologna for a quick run? I could try to arrange 
> things.

I would love to, but I have to head back for some more beam time in 
Tsukuba as soon as the experiment here ends (I do have Sunday off 
though (no beam)...


> 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"iMol,
> Dante Alighieri - Inferno - Canto XXVI
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>

Dr. Paul Fons
Senior Researcher
National Institute for Advanced Industrial Science & Technology
METI
Center for Applied Near-Field Optics Research (CANFOR)
AIST Central 4, Higashi 1-1-1
Tsukuba, Ibaraki JAPAN 305-8568

tel. +81-298-61-5636
fax. +81-298-61-2939

email: paul-fons at aist.go.jp

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