Hello, folks - In regard to Peter's question regarding multiple scattering DWFs: Matt was correct that there have been two approaches (to my knowledge) that attempt to directly address the problem: Poiarkova and Rehr's approach, and our approach. There are pros and cons to each. We (Nick Dimakis and I) have focussed on coordination complexes of metals with amino acid and similar ligands to directly address metalloproteins. The approach probably would work on other systems as well. Our method works like this: we calculate using DFT the normal modes (vibrational eigenvectors and eigenvaluesof model complexes as a function of interatomic distance and bond angles (as needed). We started this about ten years ago, and initially tried force constant models and various approximate quantum mechanical methods but found them inadequate. DFT level give sufficient accuracy and speed. Fortunately computers are fast and cheap nowadays. We have written a programs that take the eigenvalues and eigenvectors and the feff output and generates MS DWFs for each path. We have found that a "group fitting" approach works well, i.e. neglecting the inter-group multiple scattering to a first approximation. It has worked well in the cases we've tried. Since it isn't really practical to expect people to do these DFT calculations themselves (it's difficult to get convergence in many cases, it's easy to get trapped in a local minimum, and the minimization algorithms in the commercial codes are fairly antiquated), we have tried and succeeded in parameterizing the DWF for each MS path as a function of distance (and temperature). In almost all cases they are easily parameterized with polynomials as a function of both distance and temperature. So far we have done this with Zn coordinated to cysteine, histidine, and carboxylate ligands (e.g. glu), and also Cu(I) and Cu(II). We are working on Fe, Mn and other metal-ligand complexes as well, depending on funding. Hope that helps. Grant On Wed, 14 Jan 2004 ifeffit-request@millenia.cars.aps.anl.gov wrote:
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Today's Topics:
1. Spline clamps (SCalvin100@aol.com) 2. Re: Spline clamps (Bruce Ravel) 3. Re: Spline clamps (Matt Newville) 4. Debye-Waller factors for MS paths (Peter Southon) 5. RE: Debye-Waller factors for MS paths (Kelly, Shelly D.) 6. Re: Debye-Waller factors for MS paths (Bruce Ravel) 7. Re: Debye-Waller factors for MS paths (Matt Newville) 8. linux: wouldn't it be cool... (Bruce Ravel)
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Message: 1 Date: Tue, 13 Jan 2004 15:41:47 EST From: SCalvin100@aol.com Subject: [Ifeffit] Spline clamps To: ifeffit@millenia.cars.aps.anl.gov Message-ID: <1cf.17c88a73.2d35b20b@aol.com> Content-Type: text/plain; charset="us-ascii"
Hi all,
Happy New Year to all! I've been busy pushing the new versions of Artemis and Ifeffit pretty hard (3-edge fits, over 100 paths, also over 100 guess,def,set parameters) and they seem to be behaving pretty nicely. There are certainly some advantages and some disadvantages to this compared to the old FEFFIT package; one major advantage is this will certainly reduced the learning curve for new undergraduates in my group.
I am posting now because I am not sure I understand the behavior of the spline clamps in Ifeffit. When I set a top end to the spline range that is below the top of the data range, the high spline clamp has very little, if any, effect. (As a simple example, if I take the "clamp.prj" project that comes with Athena and set all of the spline ranges to top out at 400 eV, all four backgrounds look the same.) Is this what should be happening, or is this a bug?
In case this is a bug, here's the version information:
Athena 0.8.024 and ifeffit 1.2.4 running on Windows XP.
I'll also be glad to send a project file to Bruce or Matt if they wish, although it would just be the clamp.prj file with the top of the spline range changed...
--Scott