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

RE: [Ifeffit] Solution flow cells
by Irit Sagi 23 Jul '04

23 Jul '04

Dear Scott Enclosed is our NSB paper on rapid XAS of metalloenzyme + the news and views article written by J. Penner-Hahn on this article. Irit Prof. IRIT SAGI Department of Structural Biology The Weizmann Institute of Science ISRAEL Tel : 972-8-9342130 http://www.weizmann.ac.il/sb/faculty_pages/Sagi/home.html e-mail: irit.sagi(a)weizmann.ac.il >>> schlegel(a)azurite.cea.fr 23/07/04 09:45:10 >>> Scott, > I've been doing a literature search for an article I'm > writing up, and I can't seem to find any examples of an > XAS flow cell desgined for liquids. > Sealed cells for liquids, yes; flow cells for passing gases > over solids, yes; but no solution-chemistry flow cell. I > feel like someone must have published work in that area before, > but I can't seem to find it. Maybe not exactly a flow cell, but a rapid biblio research on "Web of Science" using the"stopped-flow" and "EXAFS or XAS or XANES" keywords has unearthed some 23 references over the last ten years, many of them probably utterly irrelevant. Nevertheless, I copied them in the attached text file. Best regards, Michel Schlegel

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RE: [Ifeffit] Solution flow cells
by SCHLEGEL Michel 177447 23 Jul '04

23 Jul '04

Scott, > I've been doing a literature search for an article I'm > writing up, and I can't seem to find any examples of an > XAS flow cell desgined for liquids. > Sealed cells for liquids, yes; flow cells for passing gases > over solids, yes; but no solution-chemistry flow cell. I > feel like someone must have published work in that area before, > but I can't seem to find it. Maybe not exactly a flow cell, but a rapid biblio research on "Web of Science" using the"stopped-flow" and "EXAFS or XAS or XANES" keywords has unearthed some 23 references over the last ten years, many of them probably utterly irrelevant. Nevertheless, I copied them in the attached text file. Best regards, Michel Schlegel

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RE: [Ifeffit] Solution flow cells
by Jensen, Mark P. 22 Jul '04

22 Jul '04

And just to add to Matt, Shelly, and Tsu-Chien's responses. Matt mentioned Mark Antonio's electrochemical cell. It is not a flow cell, though we did design a closely related, but unpublished, cell design for in the beam titrations. ------------------------------ 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(a)anl.gov > -----Original Message----- > From: Newville, Matthew G. > Sent: Thursday, July 22, 2004 2:55 PM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Solution flow cells > > Just to follow up on and add to Shelly's and Tsu-Chien's > responses: > > There's a paper by M. Hoffmann, et al (J. Fulton, and others > from PNNL) on a flow-cell, especially for high pressure fluids. > I believe it's in J Phys Chem (1999), but don't have the > exact citation. This might be the one Shelly saw at PNC CAT. > > Mark Antonio has a nice electrochemical cell in which he can > change both potential, but can't remember if he can flow in a > changed solution... is that "flow"? > > I believe the catalyst people who run at ESRF (esp. the DXAFS > line) have some nice flow cells too, but don't know if or > where it's published. > > --Matt > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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RE: [Ifeffit] Solution flow cells
by Kelly, Shelly D. 22 Jul '04

22 Jul '04

Hi Scott, See below: > Hi all, > > I've been doing a literature search for an article I'm > writing up, and I can't seem to find any examples of an XAS > flow cell desgined for liquids. Sealed cells for liquids, > yes; flow cells for passing gases over solids, yes; but no > solution-chemistry flow cell. I feel like someone must have > published work in that area before, but I can't seem to find it. > > So, does anyone know of any work done using a liquid-phase > XAS flow cell? Simon Bare uses a flow cell for passing liquids/gasses over a sample. This one is a glass container with kapton windows with ports for input and output. Also I have seen something like that at PNC cat. I think that Ed Stern et. al. was using it. The one at PNC cat circulated the liquid through a boron carbide section that is x-ray transparent. Shelly

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using atoms and feff
by Bruce Ravel 21 Jul '04

21 Jul '04

Hi folks, I suppose I should preface this message by saying that I will not say anything new and profound. Indeed, this email is something of a rant -- so some of you may want to click ahead to the next email right now and avoid the whole darn thing! Today I was asked a Frequently Asked Question about using atoms and feff and getting started with some fits. This particular question is pretty common, but it's one that kind of bugs me. It's been rattling around in my brain for the remainder of the evening. To get it out of my brain, I figured I would write a message to the mailing list. A colleague showed me some data and explained a bit about the sample. This person had the lattice constants and space group for the oxide form of the absorbing element but expressed a confusion about how to proceed. I asked to see the rest of the crystallographic data -- specifically the atomic positions. I was shown a printout of some stuff from webelements.com or some similar web compilation of information about the elements. Sure enough, the lattice constants were given for the oxide form, but neither complete crystallographic data nor a crystallographic reference were listed. As everyone here should know, feff requires a list of atomic coordinates as its input data. To get a feff calculation, you must tell feff where the atoms are. Ifeffit and Artemis rely upon feff to provide theoretical fitting standards, thus to start fitting you need somehow to run feff. It is a syllogism, then, that you need some kind of list of atomic coordinates before you can begin fitting with Ifeffit and Artemis. With but a passing understanding of crystallography, it should be clear that you cannot generate a list of atomic coordinates given *only* the space group and lattice constants of a crystal. The space group and lattice constants tell you the shape and size of the unit cell, but, by themselves, do not tell you what is inside the unit cell. You see, a unit cell is just like a birthday present. The box might be big and pretty, but it's not a very good present until you open it up and find out what's inside. So........ if you intend to start your analysis by using Atoms, you have to find the COMPLETE crystallographic data. Often, this is one of the more difficult parts of the analysis problem. Sometimes crystallography data is hard to find. Matt keeps a big pile of atoms.inp files on one of his web sites and that helps a lot. Many libraries have copies of Wyckoff -- that also helps a lot. Google can be awfully handy -- indeed I ended up finding the missing crystallographic data earlier today with the help of Google. Often times you will be reduced to an exhausting search through the crystallography journals looking for the data you need. Other times you will never find what you are looking for and will just have to use something similar (but not the same) as your starting point. I presume it was already abundantly clear to everyone reading this message that the space group and lattice constants by themselves are not enough to use Atoms. But I needed to vent and so availed myself of this public forum. B P.S. The question of what to do when your sample is different from its crystalline form or when your sample is not a crystal at all has been discussed several times recently. If, after reading this little rant, that's your concern, you should read and respond to one of those threads rather than to this one. P.P.S. The next time you dig through the literature to find some obscure crystal structure, save someone else the effort. Be a hero, donate the atoms.inp file to Matt's database. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 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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Artemis on Mac OSX
by POGER David 202545 21 Jul '04

21 Jul '04

Hi all I am quite new in the 'EXAFS community' and I have a problem with Artemis (v 0.7.007) on my Mac (OS X, v 10.3). When I try to load a FEFF path file (feffxxxx.dat), the program simply crashes and there's nothing I can do then, but killing the program. It creates the file 'ARTEMIS.TRAP' that I have attached. Could anyone help me? I would really appreciate your help. Thanks. David __________________________________________ POGER David Département de Réponse et Dynamique Cellulaires Laboratoire de Biophysique Moléculaire et Cellulaire Bat. K - P 215A - CEA Grenoble 17 rue des Martyrs 38054 GRENOBLE Cedex 9 FRANCE Tel: +33 (0)4 38 78 48 48 Fax: +33 (0)4 38 78 54 87 Email : david. <mailto:david.poger@cea.fr> poger(a)cea.fr

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New Comer
by jawad shah 21 Jul '04

21 Jul '04

Hi friends! I am the new commer in this field.I hope that all of you will guide and wellcome me.I am a person having no PC, With a brilliant academic record. DEar friends i hope that all of you will help me in this field. Best Regards to all friends Jawad __________________________________ Do you Yahoo!? Vote for the stars of Yahoo!'s next ad campaign! http://advision.webevents.yahoo.com/yahoo/votelifeengine/

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Re: Artemis Question
by Bruce Ravel 20 Jul '04

20 Jul '04

On Sunday 18 July 2004 11:38 pm, John Butler wrote: > Basically, the problem that I'm having is that the system I'm working > on is a solution (to start I'm trying to look at a solution of Zinc > Sulfate and then look at data with other components we're interested > in). Unfortunately, the part of the manual dealing with solution > analysis hasn't been written yet, and the people I know who use EXAFS > don't do anything with solutions. > > I was hoping that you could point me in the right direction for how to > proceed with the analysis (e.g. is there anywhere I'm likely to find > the FEFF files ... is there a 'standard' way to attack this kind of > problem). Of course I assume you're a pretty busy guy and have > neither the time nor inclination to give me a detailed step by step > guide or anything ... I was just hoping you could point me in the > right direction, give me a couple of tips, and/or show me where to > look. John, As you can see, I have forwarded you question along with my answer to the Ifeffit mailing list. You are correct to assume that I'm a busy guy. This week (like each of the other weeks this month) I am at NSLS collecting some data and helping our users. Fortunately, the mailing list is a solution to the "busy expert" problem. Enough people read and respond to the mailing list that someone should be available to answer just about every question. I doubt, actually, that you problem is really so hard to get started with. Lots of problems in XAFS do not fall into nice little pigeon holes. One knows how to deal with data on an iron foil because one knows what the structure of iron metal is. Most real research problems, obviously enough, are problems precisely because the structure is not perfectly well known. In the case of a solvated complex, there is probably some sort of analogue which can be used as a starting place. Perhaps there is some similar compound whose structure *is* known. Perhaps your solvated complex has a crystalline form that is similar, at least in the local environment, to the solvated form. In any case, find something that is similar to your real material. Run feff and compare to the data. Perhaps your analogue structure will be close to your data. In that case, you should be able to parameterize the feff calculation in such a way that you can begin to understand the ways in which your complex differs from your analogue. Perhaps the analogue structure is a very poor match for the data. That in itself is information, in that it tells you to go look for a different analogue. The common theme to what I have said here (and indeed to any analysis problem) is that you make some educated guesses as to what you real sample looks like. You test those guesses. If they seem to be leading you in the right direction, super. If not, make new (and newly educated!) guesses. My other piece of advice would be to spend some time fitting known spectra. If you are new to XAFS, then you are learning two things at the same time: how to interpret XAFS data and how to use my and Matt's screw-ball analysis programs! I consider it a good idea to spend some time fitting data for which you know the answer so that you can learn how to use the codes before plunging into the harder but more interesting problem of your own research. Good luck and join the mailing list, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 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: Athena & artemis download
by Scott Calvin 17 Jul '04

17 Jul '04

Hi Sabyasachi, It is best to address questions like this to the Ifeffit mailing list, since others may also be interested. If you are not yet a subscriber to that list, you can join at http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ I have forwarded your question to this list. I recall seeing the problem you describe before, and I think it had something to do with the updater. Try going in to your ifeffit directory and finding updater.exe. If you run that directly, you may find the updater kicks in and after grabbing about half a dozen updates, has your Artemis up to speed. --Scott Calvin Sarah Lawrence College >Scott, >I was one of the participants of this year's EXAFS short course at >BNL last month. 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 >let me know what's the best way to download the suite of EXAFS >software ? > >Many thanks in advance. > >Sabyasachi

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ParseCIF added to web page
by Kelly, Shelly D. 16 Jul '04

16 Jul '04

Hi Dave, I added your program to my little web page. Take a look see. http://146.137.194.45/exafs.html Thanks for contributing! Shelly ****************************************************************** Shelly Kelly EMAIL: skelly(a)anl.gov Argonne National Laboratory PHONE: 630-252-7376 9700 South Cass Ave. FAX: 630-252-9793 Argonne, IL 60439

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CIF to Atoms.inp-v2
by Barton, David (DG) 16 Jul '04

16 Jul '04

Users, Sorry about the resend of my previous message, but the file wasn't attached correctly so I am trying alternate mail settings to attach the file..... There have been several instances of Artemis users asking Bruce for the ability to input CIF crystallographic files directly into Artemis. In my attempt to learn Perl and produce something of value to more than one person, I wrote a program that converts CIF crystallographic files into Atoms.inp files. Bruce may implement this sometime directly into Artemis, but in the meantime I will offer the standalone, command-line conversion program to anyone who can use it. Attached is a zip file with my first version of the Perl CIF->atoms.inp file converter. The main program was snarfed from Bruce's amc2inp.pl program which converts mineral files to atoms input files. <<ParseCIF.zip>> cif2inp.pl ---main Perl program. Converts .CIF files to atoms.inp file usage: perl cif2inp.pl aucl.cif parser.pm ---parser module written by Wolfgang Bluhm of PDB at UCSD, parses CIF file into an array of hash arrays. This should be put into the STAR:: subdirectory in the perl library directory. datablock.pm ---reads the hash dictionary.pm ---dictionary of CIF terms (not used) AuCl.cif ---example CIF file from ICSD database with two records in it. The converter currently imports a single CIF file (which may have multiple CIF records) located in the \CIF directory and outputs a *.inp file for each CIF record into the \inp directory. This program has been tested with hundreds of CIF files from the ICSD and CSD databases. I cannot claim if they will work with CIFs from other sources, but I attempted to trap as many errors as I could. This program could easily be expanded to work on multiple CIF files (similar to amc2inp.pl) or...preferably....included directly in Artemis and/or ATOMS as a direct CIF file importer into these programs. I am sure there are many people that would benefit from the ability to directly open CIF files in ATOMS/Artemis and not have to worry about running a standalone application to convert their CIF files to atoms.inp files. Feel free to use any of the code that I have attached. The parser.pm and datablock.pm modules are copyrighted by UCSD (http://pdb.sdsc.edu/STAR/ <http://pdb.sdsc.edu/S! TAR/> ) but they are given away fr ee for any non-commercial use. Matt or Shelly--feel free to post the files on your websites if you see the value in sharing them. Regards, Dave _________________________________ David Barton The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA Ph: (989) 636-4753 Fax: (989) 638-9350 Email: dgbarton(a)dow.com

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CIF to ATOMS.inp
by Barton, David (DG) 16 Jul '04

16 Jul '04

Users, There have been several instances of Artemis users asking Bruce for the ability to input CIF crystallographic files directly into Artemis. In my attempt to learn Perl and produce something of value to more than one person, I wrote a program that converts CIF crystallographic files into Atoms.inp files. Bruce may implement this sometime directly into Artemis, but in the meantime I will offer the standalone, command-line conversion program to anyone who can use it. Attached is a zip file with my first version of the Perl CIF->atoms.inp file converter. The main program was snarfed from Bruce's amc2inp.pl program which converts mineral files to atoms input files. cif2inp.pl ---main Perl program. Converts .CIF files to atoms.inp file usage: perl cif2inp.pl aucl.cif parser.pm ---parser module written by Wolfgang Bluhm of PDB at UCSD, parses CIF file into an array of hash arrays. This should be put into the STAR:: subdirectory in the perl library directory. datablock.pm ---reads the hash dictionary.pm ---dictionary of CIF terms (not used) AuCl.cif ---example CIF file from ICSD database with two records in it. The converter currently imports a single CIF file (which may have multiple CIF records) located in the \CIF directory and outputs a *.inp file for each CIF record into the \inp directory. This program has been tested with hundreds of CIF files from the ICSD and CSD databases. I cannot claim if they will work with CIFs from other sources, but I attempted to trap as many errors as I could. This program could easily be expanded to work on multiple CIF files (similar to amc2inp.pl) or...preferably....included directly in Artemis and/or ATOMS as a direct CIF file importer into these programs. I am sure there are many people that would benefit from the ability to directly open CIF files in ATOMS/Artemis and not have to worry about running a standalone application to convert their CIF files to atoms.inp files. Feel free to use any of the code that I have attached. The parser.pm and datablock.pm modules are copyrighted by UCSD (http://pdb.sdsc.edu/STAR/) but they are given aw! ay free for any non-commercial use

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Atoms restraints
by Massimiliano Stola 15 Jul '04

15 Jul '04

Thank you for all the explanations about constraints for the histidine ring within Artemis. Well, I think that it will be easier, but boring, building several reasonable structures and test them one by one... I think I'll finally follow this way. I'll be interested as well in the possibility to simulate exafs data for several structures at once, like Stefano asked. It would be a nice feature for the next releases of the program! Regards Max

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Chi^2 and R-factor reporting requirements
by Stanislav Stoupin 12 Jul '04

12 Jul '04

Hello all, I would like to hear your opinion about reporting Chi^2 and R-factor values in EXAFS studies. I found that Chi^2 and R-factor values are not provided by many EXAFS papers. However, according to standards of The International XAFS Society (http://ixs.iit.edu/) both these values should be reported. My understanding is that the reduced Chi^2 should be close to 1 in ideal case. In practice however, the value is always greater than 1 because of systematic errors. For example, my reduced Chi^2 values are around 300. However, the R-factor values are about 3% which doesn't look as "ugly" as Chi^2 reduced. On the other hand, ifeffit overestimates uncertainties using reduced Chi^2 value. Thus, all errors are taken into account. The final question: Is it appropriate to report just R-factor calculated by ifeffit and the obtained uncertainties (which look reasonable) without reporting the "ugly" Chi^2/reduced Chi^2 values? Stanislav Stanislav Stoupin ----------------------------------- Research Assistant/PhD student BCPS department Illinois Institute of Technology email: stousta(a)iit.edu voice: 312-567-7983

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RE: [Ifeffit] multiple fits
by Kelly, Shelly D. 12 Jul '04

12 Jul '04

Hi Stefano, > > I have the following question: let's say I have a data set for which > I would like to try a long series of possible models and monitor the > result of the fits. The models are geometric variations of a > starting structure.I have all related feff.inp files for each model > ready. Is there a way to process the data so that I can get out the > related fits? I do not think I can do this using artemis, but maybe > there is a set of commands to be given from the command line? > > Thanks > Stefano The short answer is no. The long answer is sure. But the script that you need to write is long and complicated. You have to teach the computer how to model the structure for all the variations so that it will make the appropriate variables to determine in the fit, and also how to handle the output. These tools are not incorporated into ifeffit. I am responding to your request, because I did this as a graduate student. Back in the old days, I was using atoms, feff, and feffit. The program that I wrote moves the atoms in a unit cell, writes out a atoms.inp file, runs atoms, runs feff, makes a feffit.inp file and runs a fit, and then makes a spread sheet to compare the answers. If you are interested, I wrote is a small EXAFS paper about this script, and would be happy to share. S.D. Kelly, R. Ingalls, and E. A. Stern, "Determining crystalline atomic positions using XAFS, a new addition to the UWXAFS analysis package," Journal of Synchrotron Radiation. 8 311-313, 2001. In the end, I think that you will agree that you have a lot of work ahead of you. HTH Shelly

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multiple fits
by Stefano Ciurli 12 Jul '04

12 Jul '04

Hello, I have the following question: let's say I have a data set for which I would like to try a long series of possible models and monitor the result of the fits. The models are geometric variations of a starting structure.I have all related feff.inp files for each model ready. Is there a way to process the data so that I can get out the related fits? I do not think I can do this using artemis, but maybe there is a set of commands to be given from the command line? Thanks Stefano -- ____________________________________________ 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 "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"

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Ifeffit 1.2.6
by Matt Newville 09 Jul '04

09 Jul '04

Hi Everyone, I've posted Ifeffit 1.2.6 source code and Mac disk-image-installer today. This fixes two important bugs: 1. path lists in feffit() and ff2chi() could get polluted so that doing a second feffit() or ff2chi() using _fewer_ paths would some paths left over from the previous sum of paths. The path list is now initialized correctly. 2. reading of feff.inp with feff6 no longer fails because of line endings that don't match the standard for that platform. In addition, plot markers and arrows now support color, plot_arrow(...,color=red) plot_marker(...,color=blue) and the location of the legend in the plot window is now more customizable using either plot(...., key='data', key_x=0.9, key_y0=0.9,key_dy=0.1) or setting the variables &plot_key_x = 0.9 &plot_key_y0 = 0.9 &plot_key_dy = 0.1 where 'key_x' is the x-location of the legend, 'key_y0' is the y-location of the first key, and 'key_dy' is the vertical offset between keys. The Mac OS installer includes a pre-release of horae-037. I believe Bruce will be releasing new versions of his codes soon. When he does, we'll make a new installer for Windows as well as the usual automated update -- probably next week. Please let me know if there are any troubles with these versions, --Matt

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RE: [Ifeffit] Atoms restraints
by Jensen, Mark P. 06 Jul '04

06 Jul '04

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(a)anl.gov > -----Original Message----- > From: scalvin(a)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. > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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athena: larger data visualisation window size
by biquard xavier 06 Jul '04

06 Jul '04

Hi ! I have been using athena under LinuX with great satisfaction for a long time now. Recently, I changed my old portable computer for a brand new one: my Xwindow screen size went from 1024x768 to 1920x1250, but all windows opened by athena for data visualisation have the same old size of around 870x670: I cannot take advantage of my new screen size! As I compiled athena from scratch (horae-021), I wonder if I should not modify athena files set_properties.pl and draw_properties.pl that seems to me to be defining window size. If anyone knows for sure how to do it, please let me know! cheers, Xavier -- ------------------------------------------------------------------- Biquard Xavier Tél CEA : 0438785413 CEA-Grenoble Fax : 0438785138 DSM/DRFMC/SP2M/NRS mailto:xbiquard@cea.fr 17, av des Martyrs 38054 Grenoble Cedex 9 ------------------------------------------------------------------- 2nd chance : Tél ESRF1 : 0476882546 Tél ESRF2 : 0476882598 -------------------------------------------------------------------

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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 03 Jul '04

03 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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protein data base to feff.inp file
by Kelly, Shelly D. 02 Jul '04

02 Jul '04

Hello All, I just updated my little web page to share the protein data base file converter that I wrote. You can find the perl program and some instructions at: http://www.mesg.anl.gov/exafs.html If you use the program, let me know how it goes. Shelly > -----Original Message----- > From: Kelly, Shelly D. > Sent: Friday, July 02, 2004 9:55 AM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Atoms restraints > > > Hi Max, > > > > > 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. > > I do not understand this question. What kind of .inp file are you > looking at? Is this the input to feff? The feff.inp file needs to > have a list of atoms with their corrdinates in x, y, and z. > For a hystatine you will want to make a feff.inp file from > the crystal structure. From this list feff makes a theory > that has the contriution to the EXAFS data for each path of > the photo-electron in a different feffxxxx.dat file. Then > Ifeffit/Athena can be used to fit these paths to the data. > During the fitting process you can change the distance > between the atoms by a little bit (<0.5 Angstroms). To > change the distance during the fitting process you need to > define delr for each path included in the fit. > > I am attaching a catalase protien feff.inp file that I made > from a 7CAT.pdb file. > Hum...I see that I wrote a perl program to help do this. I > must appologize that I forgot that I had this program. > Others have asked for it in the past. > > The proceedure that I used to create this file goes like this. > 1) Get your hands on a crystal structure with the same core > hole atom. (i.e. Fe-oxide for my case) > 2) Run atoms inside of Artemis to generate a feff.inp file. > 2b) save the feff.inp file to disk. > 2c) open feff.inp file in a text editor and remove the ipot > and x,y,z coordinates. > 3) Get the pdb file for the protein, or use mine for an > example 7CAT.pdb. > 4) Save the pdf2fi.pl file to disk and the 7CAT.pdb file to disk. > 4b) make the pdf2fi.pl executable by typing "chmod 777 pdf2fi.pl" > 4c) type "pdf2fi.pl 7CAT.pdb" This will generate a > 7CAT.pdb-feff.inp file. This file has the ipot and the x,y,z > coordinates for the atoms in the pdb file. > 4d) To use the program on your own system, open pdf2fi.pl and > edit a few of the lines at the top. Don't worry it is easy > to do and you will not mess it up. You have to tell the > program what atoms are in the pdb file and which one is the core. > 5) paste the file from 4c into the feff.inp file from 2. > 6) Save the feff.inp file to disk and open it in Artemis and run feff. > > > HTH > Shelly >

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Re: [Ifeffit] Atoms restraints
by scalvin＠slc.edu 02 Jul '04

02 Jul '04

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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RE: [Ifeffit] Atoms restraints
by Kelly, Shelly D. 02 Jul '04

02 Jul '04

Hi Max, I forgot to include the perl program. Here it is. Shelly > -----Original Message----- > From: Kelly, Shelly D. > Sent: Friday, July 02, 2004 9:55 AM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Atoms restraints > > > Hi Max, > > > > > 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. > > I do not understand this question. What kind of .inp file are you > looking at? Is this the input to feff? The feff.inp file needs to > have a list of atoms with their corrdinates in x, y, and z. > For a hystatine you will want to make a feff.inp file from > the crystal structure. From this list feff makes a theory > that has the contriution to the EXAFS data for each path of > the photo-electron in a different feffxxxx.dat file. Then > Ifeffit/Athena can be used to fit these paths to the data. > During the fitting process you can change the distance > between the atoms by a little bit (<0.5 Angstroms). To > change the distance during the fitting process you need to > define delr for each path included in the fit. > > I am attaching a catalase protien feff.inp file that I made > from a 7CAT.pdb file. > Hum...I see that I wrote a perl program to help do this. I > must appologize that I forgot that I had this program. > Others have asked for it in the past. > > The proceedure that I used to create this file goes like this. > 1) Get your hands on a crystal structure with the same core > hole atom. (i.e. Fe-oxide for my case) > 2) Run atoms inside of Artemis to generate a feff.inp file. > 2b) save the feff.inp file to disk. > 2c) open feff.inp file in a text editor and remove the ipot > and x,y,z coordinates. > 3) Get the pdb file for the protein, or use mine for an > example 7CAT.pdb. > 4) Save the pdf2fi.pl file to disk and the 7CAT.pdb file to disk. > 4b) make the pdf2fi.pl executable by typing "chmod 777 pdf2fi.pl" > 4c) type "pdf2fi.pl 7CAT.pdb" This will generate a > 7CAT.pdb-feff.inp file. This file has the ipot and the x,y,z > coordinates for the atoms in the pdb file. > 4d) To use the program on your own system, open pdf2fi.pl and > edit a few of the lines at the top. Don't worry it is easy > to do and you will not mess it up. You have to tell the > program what atoms are in the pdb file and which one is the core. > 5) paste the file from 4c into the feff.inp file from 2. > 6) Save the feff.inp file to disk and open it in Artemis and run feff. > > > HTH > Shelly >

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RE: [Ifeffit] Atoms restraints
by Kelly, Shelly D. 02 Jul '04

02 Jul '04

Hi Max, > > 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. I do not understand this question. What kind of .inp file are you looking at? Is this the input to feff? The feff.inp file needs to have a list of atoms with their corrdinates in x, y, and z. For a hystatine you will want to make a feff.inp file from the crystal structure. From this list feff makes a theory that has the contriution to the EXAFS data for each path of the photo-electron in a different feffxxxx.dat file. Then Ifeffit/Athena can be used to fit these paths to the data. During the fitting process you can change the distance between the atoms by a little bit (<0.5 Angstroms). To change the distance during the fitting process you need to define delr for each path included in the fit. I am attaching a catalase protien feff.inp file that I made from a 7CAT.pdb file. Hum...I see that I wrote a perl program to help do this. I must appologize that I forgot that I had this program. Others have asked for it in the past. The proceedure that I used to create this file goes like this. 1) Get your hands on a crystal structure with the same core hole atom. (i.e. Fe-oxide for my case) 2) Run atoms inside of Artemis to generate a feff.inp file. 2b) save the feff.inp file to disk. 2c) open feff.inp file in a text editor and remove the ipot and x,y,z coordinates. 3) Get the pdb file for the protein, or use mine for an example 7CAT.pdb. 4) Save the pdf2fi.pl file to disk and the 7CAT.pdb file to disk. 4b) make the pdf2fi.pl executable by typing "chmod 777 pdf2fi.pl" 4c) type "pdf2fi.pl 7CAT.pdb" This will generate a 7CAT.pdb-feff.inp file. This file has the ipot and the x,y,z coordinates for the atoms in the pdb file. 4d) To use the program on your own system, open pdf2fi.pl and edit a few of the lines at the top. Don't worry it is easy to do and you will not mess it up. You have to tell the program what atoms are in the pdb file and which one is the core. 5) paste the file from 4c into the feff.inp file from 2. 6) Save the feff.inp file to disk and open it in Artemis and run feff. HTH Shelly

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