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@anl.gov

-----Original Message----- From: scalvin@slc.edu [mailto:scalvin@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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