[Ifeffit] Atoms restraints

[Kelly, Shelly D.]

Hi Max,

> 
> Anyway, I had a look at many .inp the examples but I did not 
> understand well 
> how to give this command to the program. Can you write me an 
> example? It would be much easier for me to start from that 
> example and add many  
> atom-atom distance restraints to keep a rigid structure. 

I do not understand this question.  What kind of .inp file are you
looking at?  Is this the input to feff?   The feff.inp file needs to
have a list of atoms with their corrdinates in x, y, and z.  For a
hystatine you will want to make a feff.inp file from the crystal
structure.  From this list feff makes a theory that has the contriution
to the EXAFS data for each path of the photo-electron in a different
feffxxxx.dat file.  Then Ifeffit/Athena can be used to fit these paths
to the data.  During the fitting process you can change the distance
between the atoms by a little bit (<0.5 Angstroms).  To change the
distance during the fitting process you need to define delr for each
path included in the fit.  

I am attaching a catalase protien feff.inp file that I made from a
7CAT.pdb file. 
Hum...I see that I wrote a perl program to help do this.  I must
appologize that I forgot that I had this program.  Others have asked for
it in the past. 

The proceedure that I used to create this file goes like this.
1) Get your hands on a crystal structure with the same core hole atom.
(i.e. Fe-oxide for my case)
2) Run atoms inside of Artemis to generate a feff.inp file.
2b) save the feff.inp file to disk.
2c) open feff.inp file in a text editor and remove the ipot and x,y,z
coordinates.
3) Get the pdb file for the protein, or use mine for an example
7CAT.pdb.
4) Save the pdf2fi.pl file to disk and the 7CAT.pdb file to disk.
4b) make the pdf2fi.pl executable by typing "chmod 777 pdf2fi.pl"
4c) type "pdf2fi.pl 7CAT.pdb"  This will generate a 7CAT.pdb-feff.inp
file.  This file has the ipot and the x,y,z coordinates for the atoms in
the pdb file.
4d) To use the program on your own system, open pdf2fi.pl and edit a few
of the lines at the top.  Don't worry it is easy to do and you will not
mess it up.  You have to tell the program what atoms are in the pdb file
and which one is the core.
5) paste the file from 4c into the feff.inp file from 2.
6) Save the feff.inp file to disk and open it in Artemis and run feff.


HTH
Shelly
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