[Ifeffit] molecule formats

Bruce Ravel bravel at bnl.gov
Mon Apr 23 12:52:01 CDT 2012


I'd like to say a few more words about this.  My answer to Eva was not
wrong and will help her over her immediate hurdle.  But it was not a
very complete or satisfying answer to her question.

The problem of converting a PDB file to a feff.inp file is a common
one.  In fact, there are a lot of ways of specifying the structure of
a molecule -- PDB is just one common way of doing so.

There is an interesting tool out there called Open Babel


OB is, among other things, a framework for converting between
different ways of specifying a molecule.  For example, OB solves the
problem of converting between PDB and Chemical Markup Language or any
of dozens of other formats.  It's very cool.

The people who wrote OB did a really good job of making it easy to add
new file formats.  The various file formats are handled by small
pieces of C++ code -- one for importing and one for exporting.

Writing those converters for Feff has long been on my list of things
to do.  Once that is done, it would be a simple matter to write an OB
interface for Artemis, allowing you to import anything that OB
recognizes as your feff input data.  Wouldn't that be great?!

This is something that somoeone with a bit of C++ knowledge could do
to contribute to the Ifeffit project.  I don't think it would take
very long and it would have a profound impact on how people use


On Monday, April 23, 2012 09:20:21 am Bruce Ravel wrote:
> > Is there an easy way to convert a PDB file into a feff.inp file? I
> > am working on a protein with a [4Fe-4S] cluster. I have generated a
> > PDB file with just the iron-sulfur cluster in it. File attached. I
> > am having a hard time with ATOMS, even when I use a single Fe atom
> > placed at the origin.
> Eva,
> See the "Molecule" section of the "noxtal.pdf" file at
>   https://github.com/bruceravel/XAS-Education/downloads
> B


 Bruce Ravel  ------------------------------------ bravel at bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973

 My homepage:    http://xafs.org/BruceRavel
 EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter

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