rotate.zip

About rotate.pl:  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.

Using rotate.pl:  This file has been zipped.  To use the code unzip it first and then make it an executable.  Using a linux system this is done by typing "unzip rotate.zip"  and then "chmod 755 rotate.pl".  Then open the file in a text editor and edit the top of the file to suite your needs.  Lots of comments have been added to the file.  You do not need to know perl to use this code. 

mkfit.zip

About mkfit.pl:  Mkfit.pl is a perl script that will take the output from running feff on a p1 space group and write equations for all the paths in terms of the unit cell dimensions and the positions of the atoms within the unit cell.  The output from mkfit.pl is in the form of a feffit.inp file and also an included file called equations.inp file.  This program needs to be adopted to write out an IFEFFIT script.

Using mkfit.pl:  This file has been zipped.  To use the code unzip it first and then make it an executable.  Using a linux system this is done by typing "unzip mkfit.zip"  and then "chmod 755 mkfit.pl".  Then type "mkfit.pl -H" to get started.  Lots of comments have been added to the file.  You do not need to know perl to use this code. 

The best way to run the program is to start in a clean subdirectory. Use TKATOMS to output a p1.inp file for the crystal structure.  Use this p1.inp file and run feff and output all the paths files.  Then type mkfit.pl.  Mkfit will output a feffit.inp file with all the delr values in terms of the variables for the unit cell.  The equations for delr are in an included file equations.inp

If you want to change some of the values for the variables that mkfit defines.  type 'mkfit.pl -t' and mkfit will output a mkfit.inp (template) file.  In this file you can change the definitions and the included paths and then mkfit will use these values/paths the next time you run it. (This is a good way to eliminate a bunch of paths that are too far away)

pdb2fi.zip 

About pdb2fi.pl:  This program will help turn a crystal database pdb file into a feff.inp file used by feff to create a theory for EXAFS data analysis. 

Using pdb2fi.pl:  This file has been zipped.  To unzip the file type "unzip pdb2.zip".  Inside the zipped file you should find 4 files.  1) pdb2.pl the perl program. 2) 7CAT.pdb file. an example pdb file.  3) 7CAT.pdb-feff.inp file the output from running "pdb2.pl 7CAT.pdb".  4) the final feff.inp file.

The procedure that I used to create the feff.inp file goes like this.

1) Make the atoms and ipot list part of the feff.inp file from the pdb file:
    a) Get the pdb file for the protein, or use 7CAT.pdb.
    c) Make the pdf2fi.pl executable by typing "chmod 755 pdf2fi.pl"
    d) 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 in a feff.inp structure.
    e) 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.  The ipot numbers need to go in order or feff will complain.

2) Make the header part of a feff.inp file.
    a) Get a crystal structure with the same core hole atom. (i.e. Fe-oxide for my case) You should be able to find one on the Atoms.inp Archive
    b) Run atoms inside of Artemis to generate a feff.inp file for the Fe-oxide.
    c) Save the feff.inp file to disk.
    d) Open feff.inp file in a text editor and remove the bottom part of the file, including the ipot section and x,y,z coordinates part of the file.

3) Paste the file from 1 into the feff.inp file from 2.
4) Save the feff.inp file to disk and open it in Artemis and run feff.

           Software written by others:

ParseCIF.zip    -By David Barton

About CIF2inp.pl:  This program reads a CIF crystallographic file from ICSD and CSD databases and then outputs an Atoms.inp file.    The program is written in Perl and runs from the command line.

Using cif2fi.pl:  Here are some instructions