[Ifeffit] Atoms restraints

[scalvin at slc.edu]

If I understand your question correctly, the answer is no. You cannot tell
Ifeffit or Artemis to constrain the distance between two atoms with a
simple command. The reason is simple--EXAFS doesn't directly contain that
information; it only contains it implicitly (maybe). For direct-scattering
paths, EXAFS only provides radial information. Multiple-scattering does
provide some information along other axes, but this causes a greater
effect in some cases than others.

What Ifeffit and Artemis do allow is for you to constrain the parameters
related to individual scattering paths in pretty much any way you desire.
So, for example, you can constrain the distance to the direct scattering
path to atom A, the direct scattering path to atom B, and the
multiple-scattering path that hits A and B in such a way that the distance
between A and B remains constant. But this takes careful geometrical
thinking on your part.

Incidentally, restraints are different from constraints. "Constraints" are
forces and cannot vary. "Restraints" penalize the fit if it drifts too
far, but allows some variation.

Hope that helps.

--Scott Calvin
Sarah Lawrence College

> So I understand that I can just tell Ifeffit/Artemis: distance between
> Atom#1
> and Atom#2 is equal to "x" Angstroms, and that will be forced for all the
> next calculations. Did I understand well??
> If this is true I believe that this way is easier than build a lot of
> structures to test (If you have more than one histidine the number of
> structures increases...).
>
> 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.
>
>