June 2004 - Ifeffit - millenia.cars.aps.anl.gov

re:fits
by k-kupiecki＠northwestern.edu 15 Jan '05

15 Jan '05

Thank you Bruce and Shelley! I just wanted to thank Matt, Bruce and everyone involved with IFEFFIT/Artemis/Athena... it has been a Godsend.... I couldn't have stumbled on it at a better time (I'm frantically trying to analyze about 4 beamtimes worth of SEXAFS data for papers and my thesis and WINXAS wasn't really working out for me)!!!!! Does anyone have any suggestions for additional literature in regards to better understanding the quality of fits and the parameters involved?.... or perhaps know when we might be able to expect a updated version of the Artemis literature? (What is currently there has helped me sooo much that I've been checking for an update every couple of weeks hoping to get see sections 2.2-3.2..... ) Also.... I guess I've realized that only knowing IFEFFIT with Artemis I kinda take things for granted (like I didn't know that IFEFFIT was having problems, in certain cases since I had only been checking the "Results" and the error messages on the bottom of the window....) which meant I missed errors like this in the IFEFFIT (since I didn't notice anything unusual in the "Results"): ............ # Do the fit! ## fitting difference of Cov_0_06ML_bl1435_111703.chi and one or more paths ... ## === data set #1 of 1 feffit(1-8, group=data0_fit, chi=data0.chi, k=data0.k, kweight=2.00, rmin=1, rmax=4, kmin=2.5, kmax=15, dk=2, kwindow=kaiser-bessel, fit_space=R, do_bkg=no, data_set=1, data_total=1) feffit fitting 1 data sets fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... no uncertainties estimated! fit gave a warning message: too many fit iterations. try again with better guesses or a simpler problem. ............................................... I guess my question is.... is there anything else I should be looking for in the IFEFFIT printout that I might not otherwise notice by just using Artemis and looking at the error messages and "Results"? Thanks for the input! Sincerely, Kristine Witkowski Northwestern University

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Athena & Artemis in Windows
by Peter Southon 22 Dec '04

22 Dec '04

Hello Windows people A few days ago Shelly suggested that Athena and Artemis don't work when installed in the directory "C:/program files/ifeffit/". This has always worked for me using XP, though I wouldn't be surprised if it caused problems in some earlier versions of Windows. Regarding Poorani's question about TRAP files, I have found it useful to put a shortcut to "C:/program files/ifeffit/horae/stash/ARTEMIS.TRAP" on my desktop or wherever for easy access. Cheers, Peter >Date: Fri, 11 Jun 2004 08:36:32 -0500 >From: "Kelly, Shelly D." <SKelly(a)anl.gov> >Subject: RE: [Ifeffit] Running FEFF >To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> >Message-ID: <1C1577844A0BDF448E14E8CCB2F74424015A1B6D(a)ANLMAIL.anl.gov> >Content-Type: text/plain; charset="us-ascii" > >Hi Poorani, > >I believe that Athena and Artemis do not work properly when installed in >the C:/program files/ifeffit directory. The installation proceedures >say to specify C:/ifeffit instead. To fix if, but all of C:/program >files/ifeffit into the trash and then re-install. > >Shelly Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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RE: [Ifeffit] Using more than one E0
by Kelly, Shelly D. 15 Dec '04

15 Dec '04

Hi Guys, I wanted to add another comment about using multiple E0's. One of the best formulas that I have found involves assigning different atom types different E0's. This method seems to work well for M.S. paths. Here is an example of how it goes. I think that Daniel Haskel was the first to publish this type of E0 stuff. "Single and multiple scattering XAFS in BaZrO3: a comparison between theory and experiment" D. Haskel, B. Ravel, M. Newville and E. A. Stern Physica B 208&209 (1995) 151 Lets pretend that we have a copper oxide that we want to model. First shell Oxygen called O1, Second shell Cu called Cu1, Third shell Oxygen called O2. This method would use three E0's. One for the first shell oxygen atoms, Eo1. One for all the Cu atoms Ecu. and one for all other oxygen atoms Eo2. The Cu-O1 path has E0=Eo1. The Cu-Cu1 path has E0=Ecu. The Cu-O2 path has E0=Eo2. The Cu-O1-Cu-O1 path has E0=Eo1, (only scattering from O1 atom). The Cu-O1-Cu1-Cu path has E0=0.5*Eo1+0.5*Ecu. (scattering once from O1 and once from Cu1) ... And so forth and so on. Now if you set something like this up. You need to look at the results carefully and see if it works. Generally, scattering from an atom that has lost an electron due to an ionic bond will have a positive deltaE, and scattering from an atom that has gained an electron will have a negative deltaE. Of course this negative/positive deltaE is added to the alignment deltaE. If the values for Eo2 and Ecu are the same within the uncertainties of the measurement then you need to make them the same variable, so then you will only have two energy shifts, but you can still use it. This is most often the case as Matt mentioned but I always like to test it out. In addition, one electron transfer is about a shift by 6 eV, so if these values differ by more than say 10 eV something is not right. Since the shift is generally smallish, say 2 eV, your fit has to be really accurate to "see" these shifts. In particular they seem to be most important when you have all the deltaR values constrained in some way so that the error in deltaR is really really small. For example all deltaR values are related to unit cell parameters and atomic positions or and overall expansion term. HTH Shelly -----Original Message----- From: Wojciech Gawelda [mailto:wojciech.gawelda@epfl.ch] Sent: Thursday, May 27, 2004 1:18 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Using more than one E0 Hi everybody, I would like to address a couple of questions which are partially related to my recent struggles in fitting some EXAFS data. I'm trying to fit my data using several shells of different neighbors including a few single scattering paths and also so multiple scattering contributions (mainly collinear multiple scattering paths) all calculated with the help of FEFF 8.20. Now, I found once in the FEFFIT manual the following suggestion: one might consider using several different E0's for different paths in order to improve the fit. Ok, the explanation was based on some approximations coming from FEFF code which include incomplete core-hole shielding, lack of angular variations of the valence charge distribution and charge transfer between atoms in polar materials. My question is the following: does anyone of you have some experience with such procedure? And if yes, shall than distinguish between the first shell of nearest neighbors and the rest of the atoms in terms of their E0 corrections (using 2 parameters)? Or perhaps one can use separate E0's for each path? That's one thing... The second question concerns the background correction in Artemis: I was trying to find an easy explanation of what this procedure does during the fit but I guess I'm still somewhat confused...how one can judge whether the spline co-refinement does the right job? Some people on this mailing list underline that one should avoid high correlations between fitting parameters and background parameters in order to make sure that the fit is correct. But is it the only criterion? In some of my fits background line looks kind of constant over the entire R-range which was taken into the fit. Sometimes it becomes like a modulation peaking underneath some scattering paths...even if the background parameters don't correlate significantly with fitting parameters I have my doubts whether the result is trustful. Any hints about this procedure? Well, I'll greatly appreciate any comments and feedback from all you guys. I hope I'll be able to share some of my own soon :-) Cheers, Wojciech ********************************************************************* Wojciech Gawelda Laboratoire de Spectroscopie Ultrarapide (LSU) Institut des Sciences et Ingénierie Chimiques (ISIC), Faculté des Sciences de Base (SB-BSP) Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne-Dorigny, Switzerland Tel.: +41 (21) 693 0452 Fax.: +41 (21) 693 0422 E-mail: <mailto:wojciech.gawelda@epfl.ch> wojciech.gawelda(a)epfl.ch WWW: <http://lsu.epfl.ch> http://lsu.epfl.ch *********************************************************************

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updating the faq with OSX-specific information
by Bruce Ravel 05 Jul '04

05 Jul '04

Hi folks, The last email got me thinking about the documentation for the various installers and updaters and such. I would like to ask one of the OSX users on the list to create a new FAQ entry in section 2 explaining how to update Athena and Artemis from source code once Ifeffit has been installed from the OSX disk image. (That is, I'd like an expert OSX user to walk the novice OSX user through the process of building from source and using sudo to install the newly built code.) Similarly, section 2 needs an entry explaining how the unix updater works. I plan to write that in the coming days. A section 2 entry from Carlo or one of the other debian users would probably be a good idea as well. Thanks, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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ifeffit and Mac OSX
by Matt Newville 04 Jul '04

04 Jul '04

Hi Raja, On Mon, 7 Oct 2002, rajasekaran swaminathan wrote: > Hi Matt, > > I tried again over the past few days to install the binary > installer on my mac (OS X.2). I couldn't find an attached aquaterm > / pgplot demo. The Aquaterm program opens, but I cannot see any > windows come out from that application. I mean, it is just like a > blank application. When I type ifeffit on Terminal app, it doesnt > recognise the presence of ifeffit in the ifeffitosx directory. i.e. > it says that the command is not found. The executable works > perfectly well on a Windows machine, and I was wondering whether > there are any such equivalents for a Macintosh machine. I also dont > think that the installer comes with athena/artemis/tkatoms etc.. Do > you have any other recommendations to resolve this issue? Also,if > it is possible, can I get a CD of these programs for a Macintosh > equivalent to an executable version for the Windows? > > I appreciate your help in this regard. I have used the binary installer once on a OS 10.1 system. It worked for me (after following the simple included instructions, of course) and plotting with Aquaterm did work. I haven't tried 10.2. I know the Mac binary installer does not include athena, artemis, or tkatoms. I believe it only provides the command-line ifeffit. I'm not sure I can answer many other questions about it. I don't know enough about it or 10.2 v. 10.1 issues to know how well it would work with 10.2. If the aquaterm/pgplot demos don't work, I'd guess it's a more serious problem and that the binary installer may not work. Is the Fink / X-Windows / PGPLOT installation procedure too big of a hassle? I know that can work, and that athena will work too. I also believe that the instructions are simpler for 10.2 than 10.1 (especially with respect to getting perl/Tk to work), but haven't tried this myself. I'm copying this message to the ifeffit mailing list, hoping that someone else may have better answers to these questions. How necessary is a complete binary installer for Mac OSX? Thanks, --Matt

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Re: Artemis download
by Bruce Ravel 30 Jun '04

30 Jun '04

On Wednesday 30 June 2004 01:39 pm, Sen, Sabyasachi wrote: > Bruce, I was one of the participants of this year's EXAFS short > course at BNL last week. It was a great course and I have learnt a > lot about the latest of what's happening in the field. I am having > trouble downloading the correct version of Artemis from the website. > I have downloaded Ifeffit 1.2.5a.exe from the website (I have > Windows 2000) and when I am trying to open Artemis it opens the 0.6 > version instead of the latest 0.7 version. Could you please point > out what I might be doing wrong and what's the best way to download > the suite of EXAFS softwares? Many thanks in advance. Sabyasachi, First off, let me repeat one thing that was said during the course: These questions are best directed to the mailing list. Helping new users solve installation problems is among the many purposes of the list. By asking a question of the list rather than of me directly, you get to tap into a much larger pool of knowledge. As you can see, I have forwarded this email to the list. The mailing list isn't the only splendid source of information available to the Ifeffit newbie. We also have a Frequently Asked Questions page at http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz The FAQ is great -- it contains tons of useful information and it's a wiki. That means that anyone in the Ifeffit community can share knowledge by authoring or editing a FAQ entry. Pretty cool! There are FAQ entries that discusses the Windows installer and updater at great length: http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=all#2.4 http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=all#2.8 If that does not help you solve your problem, post a question to the list and I am sure that one of the Windows experts who reads the list will be happy to help you out. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Re: [Ifeffit] Atoms restraints
by Matt Newville 28 Jun '04

28 Jun '04

Dear Max, > I'm a new user of the Feffit package and I have a question about > atom restraints for the fitting. > > I'm dealing with metal binding protein, and somehow I need to > keep some atoms in a fixed structure (mainly histidine rings) > while leaving a certain degree of freedom to the remaining atoms > of the environment. > > I'd like to know if there is a library containing histidine > structure restraints or if exists any input file of a similar > matter. I don't know of any such library, though such constraints and restraints could be done -- at least in principle. (I)Feffit is very strongly tied to the Sum-Of-Paths approach to EXAFS, which is not particularly good at dealing with groups of atoms as aingle entities. I believe this would be a significant amount of work. Since (I)Feffit uses a sum-of-paths and since paths (in the form of Feff's feffnnnn.dat files) do not necessarily come from a single cluster of atoms (this is by design and is a _benefit_ in many cases, though not here!), it will not necessarily be easy to identify the x,y,z coordinates of the individual atoms in a ring, let alone know that certain atoms belong together. The path to each atom would have to be identified by hand. Then, the mathematical constraints keeping the distances and angles between atoms within the ring fixed while allowing the group to move relative to the central atom would have to be worked out in terms of the allowed motions. To be honest, I haven't really thought about how to do this in any detail. --Matt

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RE: [Ifeffit] Atoms restraints
by Kelly, Shelly D. 27 Jun '04

27 Jun '04

Hi Matt, My program for rotating a phosphate group can be easily modified to rotate any group of atoms. The problem being that you need to know a little bit of perl to do it. The top part of the perl script has a lot of comments showing you where you would want to make these changes. Basically you have to tell the program where all the atoms are and how you want to rotate them. I could easily modify the script to run from an input file, but it seems like I should write a gui interface to the program so that it would be more user friendly...hum..? I wonder if PGplot could be used to display a ball and stick model and then be used to transfer information back and forth from perl? Would anyone be interested in helping me figure that part out? Shelly > -----Original Message----- > From: Stefano Ciurli [mailto:stefano.ciurli@unibo.it] > Sent: Sunday, June 27, 2004 12:41 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Atoms restraints > > > Dear Matt, > > I also had asked a similar question some time ago, and Bruce said > that it should be easy to build such restraints using his programs. I > asked the question because I have several colleagues working with > EXCURVE, a program that implements the histidine ring as a group and > modifies distance and orientation with respect to the scattering atom > to which it is bound. I do not want to use EXCURVE for several > reasons, and I like FEFF much better. There must be people out there > in the mailing list that deal with biological samples, most often > containing a histidine ring bound to a metal ion, and use ifeffit. I > think the question that Max asked should be dealt with in detail. I > think that many more people would use these programs if a routine for > histidine ring would be implemented. Some time ago Shelly Kelly > proposed one of her programs to rotate a phosphate group bound to a > metal ion, and the program was made available. This is the kind of > things, that, when implemented by experienced people like many in > this list, would help many non-experienced people in this list. > > Another possibility is of course to build several models of M(His)n, > with varying the number of histidines and their distances and angles. > So far, this is the best I could think of. > > Stefano > > >I don't know of any such library, though such constraints and > >restraints could be done -- at least in principle. (I)Feffit is very > >strongly tied to the Sum-Of-Paths approach to EXAFS, which is not > >particularly good at dealing with groups of atoms as aingle entities. > > > >I believe this would be a significant amount of work. Since > (I)Feffit > >uses a sum-of-paths and since paths (in the form of Feff's > feffnnnn.dat > >files) do not necessarily come from a single cluster of > atoms (this is > >by design and is a _benefit_ in many cases, though not > here!), it will > >not necessarily be easy to identify the x,y,z coordinates of the > >individual atoms in a ring, let alone know that certain atoms belong > >together. The path to each atom would have to be identified > by hand. > >Then, the mathematical constraints keeping the distances and angles > >between atoms within the ring fixed while allowing the group to move > >relative to the central atom would have to be worked out in terms > >of the allowed motions. To be honest, I haven't really thought > >about how to do this in any detail. > > > >--Matt > > > > > >_______________________________________________ > >Ifeffit mailing list > >Ifeffit(a)millenia.cars.aps.anl.gov > >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > -- > ____________________________________________ > > Stefano Ciurli > Professor of Chemistry > Department of Agro-Environmental Science and Technology > University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy > Phone: +39-051-209-6204 > Fax: +39-051-209-6203 > > "Fatti non foste a viver come bruti, > ma per seguir virtute e canoscenza" > Dante Alighieri - Inferno - Canto XXVI > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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Atoms restraints
by Massimiliano Stola 25 Jun '04

25 Jun '04

Hi, I'm a new user of the Feffit package and I have a question about atom restraints for the fitting. I'm dealing with metal binding protein, and somehow I need to keep some atoms in a fixed structure (mainly histidine rings) while leaving a certain degree of freedom to the remaining atoms of the environment. I'd like to know if there is a library containing histidine structure restraints or if exists any input file of a similar matter. Looking forward to hearing from you Max

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Re: [Ifeffit] Re: A very quick question
by Scott Calvin 19 Jun '04

19 Jun '04

Dave wrote: >And....one other feature request for Bruce for Athena version 2.3. It would be nice if we could put constraints on each of the fitting variables. This would help prevent fits where the variables quickly spin off into meaningless territory. Of course, implemenation of this feature could get complex given the number of variables to be fit. An easier implemenation of constraints would be a checkbox and a % deviation field that would let the variables chosen float within that %deviation. >> Ifeffit (and thus Artemis) already has "max" and "min" features that allow you to approximate this. For example, to require S02 to be between 0.60 and 1.00, you can do the following: guess S02p = 0.80 def S02p = max(0.60,min(1.00,S02p)) Admittedly that is a bit awkward, and Bruce could implement it as you suggest in Artemis. My experience is, however, that this does not work very well. A fit which likes to "spin off" tends to pin itself to one of the edges of the allowed range anyway, and then the ifeffit routines for working out uncertainties and correlations lose their ability to figure out what is going on (the fitted parameter can become in some sense meaningless to the fit). So I think if Bruce implements it that it would just be a source of frustration. You could use "restraints" instead, although that raises its own issues of defensibility and how to choose the weighting function. My preference is to find other ways to make the fit conform to the real world, e.g. I include more paths, or more k-weights, or other constraints, or values from a standard... --Scott Calvin Sarah Lawrence College

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