[Ifeffit] protein data base to feff.inp file

[Kelly, Shelly D.]

Hello All,

I just updated my little web page to share the protein data base file
converter that I wrote.  You can find the perl program and some
instructions at: 
http://www.mesg.anl.gov/exafs.html

If you use the program, let me know how it goes.
Shelly

> -----Original Message-----
> From: Kelly, Shelly D. 
> Sent: Friday, July 02, 2004 9:55 AM
> To: XAFS Analysis using Ifeffit
> Subject: RE: [Ifeffit] Atoms restraints
> 
> 
> 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
>