[Ifeffit] graphics and fit

[Bruce Ravel]

On Thursday 13 May 2004 06:30 am, Stefano Ciurli wrote:
> Hello,
>
> just a thought: wouldn't it be nice to be able to read the feff.inp
> file directly into a simple molecular graphics program in order to
> see if the used coordinates contain any error? Maybe it is possible
> already and I am not aware of it. I understand that the program is
> mainly used by material scientists, but for us working with
> biological samples of metalloproteins it would be nice.
> Another suggestion: I know that Excurve is able to treat the
> histidine rings as a unity, and when performing the fit that program
> is able to maintain the ring rigid while fitting the distance between
> the metal and the imidazole ring of the histidine. How can I do that
> simply using your suite?
>
> Stefano

The notion of having a viewer of ball-and-stick images built into the
software is not a new one.  Indeed that's part of Cerius and, as I
recall, EXAFSPAK does that as well.  Maybe others, too.

I agree that it's an excellent idea and I certainly understand the
value of it.  But I don't plan on working on such a tool any time
soon.

Then Mauro wrote:

>With tkatoms you can save your feff.inp in .pdb format and open it with
>RasMol.

This is correct.  Atoms already converts crystallographic data into
pdb (and other formats).  This can be done with command line atoms,
TkAtoms, or Artemis. (And WebAtoms, in principle.  It would be easy to
do if it doesn't already, which I can't remember one way or the
other.)  Indeed, any version of atoms can be coerced into writing just
about any file for use with a molecule viewer just by creating an
appropriate template file.

Then Stafano wrote:

> it would be nice to be able, with Tkatoms, to read coordinates from 
> pdb files and output feff.inp files... but maybe this will come.

That question is the exact opposite of your original question.  Indeed
reading pdb files is one of my eventual goals for Artemis.

One could jump-start that effort by showing me how it's done,
preferably (but not necessarily) in perl.

In any case, it's not rocket science to make a feff.inp from a PDB.
Look at page 19 of this for an example using a very small PDB:
  http://cars9.uchicago.edu/xafs/NSLS_EDCA/Sept2002/Ravel.pdf
And remember, Feff does NOT require the absorber to be at (0,0,0).

B

-- 
 Bruce Ravel  ----------------------------------- ravel at phys.washington.edu
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