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

Re: Athena & artemis download
by Scott Calvin 18 Jul '04

18 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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