[Ifeffit] Atoms restraints

Fri Jul 2 12:00:21 CDT 2004

Here are my 2 cents worth on how to constraint the histidine ring within
Artemis.

Don't lose heart, Max. Both Scott and Bruce are right. There is no
simple command to hold two scattering atoms in a particular relationship
in Ifeffit, but the problem is easily solvable for this system partly
because multiple scattering paths won't be too important and partly
because the ring is quite rigid. (Actaully based on my experience with
other organic ligands, the non-coordinated atoms in the histidine ring
is probably not too important for EXAFS, but if you want to use the
whole ring, this is how I would approach the problem using information
external to the EXAFS data.)

The histidine ring is a 5-membered (planar) aromatic ring, with 2
nitrogens and 3 carbons. That makes visualizing things a lot easier.
Off-hand, I don't know what the bond lengths and bond angles within the
ring are, but you could find that information from x-ray crystal
structures of histidine complexes and it would be contained in the
feff.inp file (which you could make using the procedure Shelly Kelly
distributed to the list morning). But, somehow you have to build a
feff.inp file and do the feff calculations so you have some paths to
fit.

Assuming that the absorbing atom , "M", is at coordinates (0,0,0) makes
things simpler. Fortunatley that should be the case for a feff.inp file.

You will have to define at least 17 new "set" variables in Artemis, one
x, y, and z coordinate for each of the 5 atoms in the ring, as well as
the angles theta and phi. The x,y,z coorinates have to be manually input
from the feff.inp file. You will also need some other variables to hold
intermediate coordinates, for example del_x, del_y, and del_z.

As Scott pointed out, EXAFS is mostly sensative to the radial distance,
and our case that's exactly what Artemist/Ifeffit is varying by adding
del_r to the scattering path length. What you want to do is move the
other 4 atoms of the histidine ring in conjunction with the del_r
changes in the M-N bond length.

First, convert the x,y,z coordinates of the coordinated nitrogen atom
(I'll call these (xN, yN, zN) ) to spherical coordinates (r_eff, theta,
phi). You need to put the values of theta and phi into the Guess,Set,Def
parameters as set parameters because you will need them later to convert
from spherical coordinates back to regular 3D-rectangular (x,y,z)
coordinates. In the fitting, the changes in the M-N single scattering
path length (i.e., the M-N bond distance) will not effect the two angles
theta and phi for the coordinated N. However, changing the M-N distance
will change theta and phi (relative to the absorbing atom) for the other
4, so there is some algebra to do.

Now this is where the whole approach might fail. I don't know if it is
possible to to incorporate the delr or the delr+reff value from a
specific feff path into an algebraic expressions in the Guess,Set,Def
panel. Bruce or Matt or someone else will have to comment on this and
explain how to do it. However, assuming that there is a straigforward
way to do it, then...

for each iteration of the fit in Ifeffit/Artemis there is a particular
M-N distance for the scattering path of the coordinated histidine
nitrogen, Artemis calls this "r" (for each path) and it is equal to
reff+delr for each path (also using the Artemis nomenclature). Using
theta and phi (which haven't changed for the coordinated N) and "r", a
new set of coordinates in regular space (x_new,y_new,z_new) for the
coordinated nitrogen can be calculated within Artemis using the standard
equations for spherical coordinates. (Like I said, if we can't access
"r" from the alegbraic expressions in Guess,Set,Def this won't work,
though).

Then, taking the difference of the current position and the original
position of the coordinated nitrogen in x,y,z coordinates, we get
(del_x,del_y,del_z). In other words del_x = (x_new - xN) can be defined
as a DEF parameter in the Guess,Set,Def panel. This single set
(del_x,del_y,del_z) vector is going to be added to the (x,y,z)
coordinates of each of the 4 other atoms in the histidine ring to get
their current coordinates in the next and final step.

Finally, to get the change in the radial distance of each of the 4 other
ring atoms, put the expression
[(x_orig+del_x)^2+(y_orig+del_y)^2+(z_orig+del_z)^2]^0.5 -
[x_orig^2+y_orig^2+z_orig^2]^0.5  in the "delr" blank (where
[x_orig^2+y_orig^2+zorig^2]^0.5 is actually reff for the path) for each
of the 4 feff paths of the 4 non-coordinated ring atoms. In this
equation, "x_orig" is the original x-coordinate of the non-coordinated
ring atoms and "del_x" was calculated from the new position of the
coordinated nitrogen atom above.

Things can get trickier if you want to incorporate multiple scattering
paths, but I think that woiuld probably not be a fruitful line of
inquiry anyway. If you stick to singlescattering paths, that's all there
is to it! ;)

Good Luck,
Mark Jensen

------------------------------
Mark P. Jensen
Chemistry Division
Argonne National Laboratory
9700 South Cass Avenue
Argonne, Illinois  60439-4831
USA
630-252-3670
630-252-7501 FAX
mjensen at anl.gov

> -----Original Message-----
> From: scalvin at slc.edu [mailto:scalvin at slc.edu] 
> Sent: Friday, July 02, 2004 9:19 AM
> To: XAFS Analysis using Ifeffit
> Subject: Re: [Ifeffit] Atoms restraints
> 
> 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.
> >
> >
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