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

Atoms restraints
by Massimiliano Stola 02 Jul '04

02 Jul '04

Thank you guys for your answers, Bruce, you said: "The central point here is that Ifeffit (and by extension, Artemis) allows you to write such things as the distance between atoms in the form of an almost arbitrary algebraic expression." 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. Thank you very much Max

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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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two comments
by Bruce Ravel 19 Jun '04

19 Jun '04

Hi! Just now I was reading through some of the mail I missed while away at a conference and I have a few general comments. 1. Doug Pease had some problems with Artemis being bigger than the size of his screen. This is a problem I am aware of, but haven't got around to fixing. All my GUI codes are written assuming that your screen is at least 1024x768. They just don't display properly at lower resolution. Similarly, there is an option under Windows XP for using fonts larger than normal for the specified resolution. That is, you can set resoution at 1024x768 but have windows use scaled up fonts such that, say, a 10pt font would display as if the resolution were 800x600. This feature is nice those with untrustworthy eyes, but my GUI codes play poorly with this. Bottom line: to use my codes you need to set your resolution to 1024x768 or higher and not use the scaled up fonts. My apologies to anyone stuck with weak eyes or a old monitor. 2. Lots of people have complained trap files being written to a place that includes this string: __ENV__IFEFFIT_DIR. Although people reported several different situations, everytime you see that string, it is the same bug. I am aware of this bug and I think I have fixed it. I am going to try to get a new version out sometime during the week of June 27th. 3. Peter Southon made a very clever suggestion one day which I would like to modify just slightly. Make a desktop shortcut to C:/Program Files/Ifeffit/horae/stash/ This will allow you to quickly find trap files written by Athena and Artemis and also to very quickly find Artemis' workspace. Ta ta, 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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a few words...
by Bruce Ravel 18 Jun '04

18 Jun '04

Hi folks, This is just a quick note to let everyone know that I have read all of the traffic on the mailing list from the last two weeks. Clearly there are some serious issues with the current release of artemis that need my attention. I am still in the middle of a very busy period and won't have much time to devote to the codes for a couple more weeks, but I wanted everyone to know that I have read about the problems and will work on solutions just as soon as I get a chance. Thanks to those who commented for your input. As I have said many times before, the codes are only usable because of the contributions of their users. It seems that most of the non-bug report traffic was answered to some extent. I probably will not respond to any of the mail from the last two weeks, so if anyone posted a question for me that didn't get answered to your satisfaction, I would recommend posting it again. I also wanted to comment on a couple of things that made me laugh out loud. One was was Paul's comment to Chris Derr asking him to inform the list of the answer once he gets EXAFS all figured out. (Is it 42?) The other was when Doug Pease (sorry for picking on you Doug, but this *was* funny) refered to Shelly Kelly as Mary Shelly. Mary Shelley, of course, was the author of Frankenstein. I would say that it is unfair to burden Shelly with the responsibility of creating a Frankenstein monster. That would be me or Matt, I think, depending on whether the interior part or the exterior part seems more monstrous to you ;-) 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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Fwd: Alignment!
by Bruce Ravel 18 Jun '04

18 Jun '04

Hi folks, I received this (rather vague) question this morning and thought I would forward it along to the list for discussion. A couple of FAQ entries seem relevant: http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=all#5.6 and http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=all#5.7 Perhaps someone could write a FAQ entry on the topic of data alignment... B ---------- Forwarded Message ---------- Subject: Alignment! Date: Friday 18 June 2004 10:20 am From: Nasser Afify <n_afify(a)science.unitn.it> To: ravel(a)phys.washington.edu Dear Prof., I need to align my fluorescence spectra to the one of the reference before the extraction of the signals, but it is too difficult to align, what is the best way for alignment and what is the best choice of E0 in the case of noisy data. thank you for your time best regards, Yours Nasser ------------------------------------------------------- -- 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: A very quick question
by Barton, David (DG) 18 Jun '04

18 Jun '04

On Thursday 17 June 2004 03:17 pm, Ahmed M Shahin wrote: AM> Hello, I would like to ask a very quick question and I would AM> appreciate if someone can help me. While running XANES fitting AM> for mixed valence state metals such as cerium (3/4), should I use AM> two arctangent functions with selected group of Lorentzian AM> functions or I have to use only one arctangent function with a AM> group of Gaussian functions? I would appreciate if someone give AM> some advice. Yours, Ahmed I have used the XANES peak fitting option some in Athena and would concur with Bruce's suggestions that peak fitting needs to be handled in a *consistent* manner to be useful. With that said, I appreciated Bruce adding the feature to be able to fit multiple arctangents because it can help tease out the relative ratios of mixed valence state metals. However, one must be careful to not overinterpret these fits because of the sensitivity of the XANES edges to coordination changes as well as oxidation state. With the appropriate set of standards this fitting can be a useful tool especially when the data quality does not permit a full blown EXAFS analysis. In regards to the other peak shapes (Lorentzian or Gaussians)....use what fits best. This fitting is just a tool to help describe your datasets and is not a fundamental approach to XANES interpretation. One other suggestion, be patient with the fitting and play around. Try multiple initial guesses, don't let all variable float in the initial fit, consider fitting the energy first and then fix it and fit the other variables. Once you get a good fit, use this solution as the initial guesses for all your other datasets. 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. Dave _________________________________ David Barton The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA Email: dgbarton(a)dow.com

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