- 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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Regarding XANES spectra of Manganese oxides
by Grant Bunker 17 Jun '04

17 Jun '04

This is in response to Prof. Gang Ho Lee's question. There is indeed a spinel form of Mn2O3 which is isostructural with Mn3O4, except (as I recall from twenty years ago) that the +2 and +3 ion populations are reversed (2/3 of the ions are in octahedral sites, and 1/3 in tetrahedral). So even though the average charge state is changed, the structure isn't. The XANES and XRD are virtually the same because the structures are virtually the same. grant bunker On Thu, 17 Jun 2004 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: a few words... (scalvin(a)slc.edu) > 2. A very quick question (Ahmed M Shahin) > 3. Re: A very quick question (Bruce Ravel) > 4. Reagrding Xanes spectra of manganese oxides (Gang Ho Lee) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Jun 2004 14:01:28 -0400 (EDT) > From: scalvin(a)slc.edu > Subject: Re: [Ifeffit] a few words... > To: ravel(a)phys.washington.edu, "XAFS Analysis using Ifeffit" > <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <2823.138.110.111.207.1087495288.squirrel(a)mail.slc.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Bruce said: > > > 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?) > > > > Bruce! I'm shocked at you! Everyone knows that legitimate EXAFS results > must always be reported with the uncertainty; the answer is actually 42 > +/- pi. > > --Scott Calvin > Sarah Lawrence College > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Jun 2004 14:17:38 -0500 > From: "Ahmed M Shahin" <shahin(a)umr.edu> > Subject: [Ifeffit] A very quick question > To: <Ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <001a01c4549f$c0ece3a0$fc689783(a)chem.umr.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > I would like to ask a very quick question and I would appreciate if someone can help me. > While running XANES fitting for mixed valence state metals such as cerium (3/4), should I use two arctangent functions with selected group of Lorentzian functions or I have to use only one arctangent function with a group of Gaussian functions? > I would appreciate if someone give some advice. > Yours, > Ahmed > >

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Reagrding Xanes spectra of manganese oxides
by Gang Ho Lee 17 Jun '04

17 Jun '04

Dear Sirs I am writing to you because we are not familiar with xanes. We took xanes spectra of both sample (synthesized by us and we think it as gamma-Mn2O3 ) and Mn3O4 (reference) to make sure that we synthesized gamma-Mn2O3 nanoparticles. The particle diameters ranged from 10 to 15 nm. By using XRD pattern, the structure of sample was determined to be tetragonal with lattice constants of a=5.79 A and c=9.4 A, similar to Mn3O4. From the XRD patterns, we can not distinguish between gamma-Mn2O3 and Mn3O4 because both show nearly identical XRD patterns (JACS 72, 856 (1950)). We attached a data file. Could you please tell us whether the sample is gamma-Mn2O3 nanoparticles or not. Sincerely, Prof. Gang Ho Lee Department of Chemistry College of Natural Sciences Kyungpook National University Taegu 702-701, South Korea tel: 001-82-53-950-5340 fax: 001-82-53-950-6330 e-mail: ghlee(a)bh.knu.ac.kr

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A very quick question
by Ahmed M Shahin 17 Jun '04

17 Jun '04

Hello, I would like to ask a very quick question and I would appreciate if someone can help me. While running XANES fitting for mixed valence state metals such as cerium (3/4), should I use two arctangent functions with selected group of Lorentzian functions or I have to use only one arctangent function with a group of Gaussian functions? I would appreciate if someone give some advice. Yours, Ahmed

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Artemis: Error in laoding additional FEFF paths?
by Carlo U. Segre 17 Jun '04

17 Jun '04

Hello All: One of my students is just trying Scott's ZnO tutorial and we are finding a consistent problem when trying to work with the third project file. When we get to the point of adding an additional path, (feff0011.dat), artemis crashes with the following message: --------------------------------- The following message was trapped by Artemis: Artemis0.7.006warn/home/segre/.horae/stash/ARTEMIS.TRAPCODE(0x9652e54)/home/segre/.horae/stash/artemis.project.2/ at /usr/bin/artemis line 1562 main::__ANON__('Use of uninitialized value in string eq at /usr/bin/artemis l...') called at /usr/bin/artemis line 7313 main::read_feff('^^') called at /usr/lib/perl5/Tk.pm line 225 eval {...} called at /usr/lib/perl5/Tk.pm line 225 Tk::__ANON__('Tk::Menu=HASH(0x974a060)', 'active') called at /usr/lib/perl5/Tk/Menu.pm line 531 Tk::Menu::Invoke('Tk::Menu=HASH(0x974a060)', 1) called at /usr/lib/perl5/Tk.pm line 347 eval {...} called at /usr/lib/perl5/Tk.pm line 347 Tk::MainLoop() called at /usr/bin/artemis line 1707 -------------------------------- This is happening on all of my Linux machines. They are using my Debian packages and so I have not tried with the tarball installation. Has anyone else had this problem? I hesitate to report it as a bug until it is confirmed. In a previous version of horae, it worked fine. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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Re: [Ifeffit] Iffeffit1.5.2a compilation troubles
by Stefano Ciurli 16 Jun '04

16 Jun '04

Hello folks, I said earlier: "Apparently, I need to restart the PC any time that somethig goes wrong with aquaterm" No, the problem is really with the ZnO tutorial .apj files. I get aquaterm starting when I open a Cu.chi file, but I do not get it to open when I try to read the ZnO1.apj file. I think this is due to some bug in horae, which makes the programs not really good at managing project files. I think Bruce said something like that some time ago. 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

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Re: [Ifeffit] Iffeffit1.5.2a compilation troubles
by Stefano Ciurli 16 Jun '04

16 Jun '04

Hello folks, following the "lost" message from yesterday, and in order to solve the apparent bug that aquaterm does not start automatically etc etc, I reinstalled 1.2.5a using the binary installer AND, this time, restarted the computer (the same old trick). This time aquaterm opens again.... Then, after running the horae_update --force command, aquaterm does not open automatically. BUT, if I restart again the PC, the aquaterm opens. Apparently, I need to restart the PC any time that somethig goes wrong with aquaterm. 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

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Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 15 Jun '04

15 Jun '04

Matt, as to the following question: QUESTION: I do not seem to have, in tcsh, the command "configure" I think I solved this one by entering the /Users/stefano/Tk-804.027/ifeffit-1.2.5 directory I am proceeding with the resto of the indicated protocol, so far not caring about the downloading directory (I am using my home directory right now). Please let me know whether I can change the Tk-804.027 directory from my home directory to where it is more right to move it (which I do not know). 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

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Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 15 Jun '04

15 Jun '04

Paul, this is my .cshrc file: bindkey -k up history-search-backward bindkey -k down history-search-forward if (! $?DISPLAY) then setenv DISPLAY :0.0 endif source /Library/Scripts/iterminal_custom.tcsh source /sw/bin/init.csh source /Users/stefano/Programs/XtalView/XtalView.env setenv PATH `echo $PATH`:/usr/local/sparky/bin:/usr/local:/usr/local/molscript:/usr/local/bin:/Users/stefano/Programs/modeller6v2:/Users/stefano/Programs/o/bin/:/Users/stefano/Programs/autodock/dist305/bin:/Users/stefano/Programs/autodock/dist305/share/:/Users/stefano/Programs/Validation_suite/validation-v0.904-beta-prod-bin-darwin/bin:/Users/stefano/Programs/XtalView/bin/powerpcDarwin5/ defaults write com.apple.x11 wm_ffm true defaults write com.apple.x11 no_quit_alert true setenv RCSBROOT /Users/stefano/Programs/Validation_suite/validation-v0.904-beta-prod-bin-darwin setenv SPARKYHOME /Users/stefano/Programs/Sparky setenv EDENHOME /usr/local/eden setenv ODAT /Users/stefano/Programs/o/data setenv PGPLOT_DIR /etc setenv PGPLOT_DEV /AQT source /Library/Scripts/settitle.csh source /Users/stefano/Programs/NMRPipe/com/nmrInit.mac.com alias ono osx_ono ### begin MODELLER6v2 ###################################################### setenv MODINSTALL6v2 /Users/stefano/Programs/modeller6v2 setenv EXECUTABLE_TYPE6v2 mac10v2-absoft setenv LIBS_LIB6v2 $MODINSTALL6v2/modlib/libs.lib setenv KEY_MODELLER6v2 MODELIRANJE alias mod mod6v2 set path=($path $MODINSTALL6v2/bin) limit stacksize unlimited ### end MODELLER6v2 ######################################################## # this line was added by Ifeffit Installation Script source /Applications/Ifeffit/bin/iff_init.csh ~ so I think I do have the instruction for aquaterm. It is not a very nasty bug. I just have to remember to start aquaterm first... and the only bugging idea is that it worked once... Ciao, Stefano > In my case, aquaterm opens automatically. I did set in my .cshrc >(shell script initialization file), the variable >PGPLOT_DEV=/AQT >I do know that aquaterm started even automatically even when I was >building horae using the pgplot in fink as well. > > Paul -- ____________________________________________ 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

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Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 13 Jun '04

13 Jun '04

Hello Matt, after having installed 1.2.5a, the aquaterm is now opening ok: am currently trying artemis ZnO tutorials... 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

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Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 13 Jun '04

13 Jun '04

Hello again, after running horae_update, and having now horae-036, I still do not get aquaterm to open.... SHould I reinstall ifeffit1.2.5a??? Trying to do so... 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

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Re: PCA
by Webb, Samuel M. 12 Jun '04

12 Jun '04

Hi Ethan, Glad to hear you've been checking out the PCA routines in SixPACK. I'm away from the office until after the July 4th holiday, so email access will be a little impeded. Your're right, the "save component" menu feature doesn't work, much to my surprise. I'll have this fixed in my next release. However, until that time (I won't be able to make an improved version until post July 5th), here is a quick work-around. You can plot the components, then use the "copy plot data to clipboard" option in the plot menu. This will place all current plots on the clipboard, which can then be pasted into any other application you'd like for further examination. If you want to save the components for further use in Sixpack or Athena/Artemis, any 2 column ascii format will work. As for the target transform, I can put that information of that fit into the next relase as well. As a temporary fix again, you can take the saved components (saving each of the plots above into its own text file) and then do a linear combo fit to get that data, using the PCA components as the components and the target transform file as the sample. This should give you the same fit as the target transform does in the PCA routine. Thanks for the feedback. Its always good to get comments from other users -- particularly on things that I didn't think of on the first time around. I'll try to have those improvements in the PCA released when I get back to my office. Sam ******************************************** Sam Webb SSRL/SLAC Bldg. 137, MS 69 2575 Sand Hill Rd. Menlo Park, CA 94025 Phone: (650)-926-3734 FAX: (650)-926-4100 E-mail: samwebb(a)slac.stanford.edu *******************************************

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trying to run artemis again
by doug pease 11 Jun '04

11 Jun '04

Hi Scott, This may duplicate the essentials of another e mail I sent to an address I found at the Sarah Lawrence home page, which looks a little different from this address. I would be delighted if you could look at my problem with ARTEMIS, and thank you for the generous offer!. My computer is presently at my home on 140 Sawka Drive, East Hartford, Connecticut, 06118. My phone is 860 - 568 - 5055. Once the bugs are out of these programs enough so that I can do a basic analysis, and I know I won't need to download anything I will move this computer to U. Conn. (My U. Conn. computer will only support 98, whereas my home computer supports XP. The home computer is closer to working with these programs than the one at U. Conn.) My home is about 35 minutes further from Holyoke and 35 minute closer to New Haven than U. Conn. Anytime is great for me except during the work day on Friday next week the 18th, when I have TEM time. We will cook for you if you wish, and thank you so much! Let me know the best time for you. Sincerely, Doug

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RE: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Kelly, Shelly D. 11 Jun '04

11 Jun '04

Hi Carlo, Bruce is away. I'm sure that he fix this bug when he gets back. Shelly > -----Original Message----- > From: Segre, Carlo U. > Sent: Friday, June 11, 2004 9:15 AM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Artemis: Error in laoding additional > FEFF paths? > > > > > Shelly: > > Reading them in all at once is not a problem. It is just > when you read 10 in at once and then try to add another one > that we get problems. Specifically, Scott's ZnO tutorial does > this and has given light to the bug. > > I think that if one does as you propose, there is no problem > and artemis is functional. > > Carlo > > On Fri, 11 Jun 2004, Kelly, Shelly D. wrote: > > >Hi Carlo, > > > >Here is something to try. Put all the feffxxxx.dat files > into a single > >directory. Rename them so that you do not have repeating numbers. > >Then try to read them in all at one time. > > > >Shelly > > > >> -----Original Message----- > >> From: Stefano Ciurli [mailto:stefano.ciurli@unibo.it] > >> Sent: Thursday, June 10, 2004 3:12 PM > >> To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > >> Subject: Re: [Ifeffit] Artemis: Error in laoding additional FEFF > >> paths? > >> > >> > >> Carlo, > >> > >> I have been having consistent problems running the tutorials on my > >> MacOSX G4 portable PC. I have posted several times the tect of the > >> trap files I am getting. .Apparently, there is no definitve answer > >> (yet). I am sure Bruce will try to clean up things whenever he has > >> time. But, if for some reason, some of you out there knows > a way out, > >> I'll be one of the many to be happy to read it. > >> > >> Stefano. > >> > >> >One of my students is just trying Scott's ZnO tutorial and we are > >> >finding a consistent problem when trying to work with the > >> third project > >> >file. > >> > > >> >When we get to the point of adding an additional path, > >> (feff0011.dat), > >> >artemis crashes with the following message: > >> > > >> >--------------------------------- > >> > > >> >The following message was trapped by Artemis: > >> > > >> >Artemis0.7.006warn/home/segre/.horae/stash/ARTEMIS.TRAPCODE(0 > >> x9652e54)/ > >> >home/segre/.horae/stash/artemis.project.2/ > >> >at /usr/bin/artemis line 1562 > >> > main::__ANON__('Use of uninitialized value in > string eq at > >> >/usr/bin/artemis l...') called at /usr/bin/artemis line 7313 > >> > main::read_feff('^^') called at > >> /usr/lib/perl5/Tk.pm line 225 > >> > eval {...} called at /usr/lib/perl5/Tk.pm line 225 > >> > Tk::__ANON__('Tk::Menu=HASH(0x974a060)', > 'active') called > >> >at /usr/lib/perl5/Tk/Menu.pm line 531 > >> > Tk::Menu::Invoke('Tk::Menu=HASH(0x974a060)', 1) > called at > >> >/usr/lib/perl5/Tk.pm line 347 > >> > eval {...} called at /usr/lib/perl5/Tk.pm line 347 > >> > Tk::MainLoop() called at /usr/bin/artemis line 1707 > >> > > >> >-------------------------------- > >> > > >> >This is happening on all of my Linux machines. They are using my > >> >Debian packages and so I have not tried with the tarball > >> installation. > >> > > >> >Has anyone else had this problem? I hesitate to report > it as a bug > >> >until it is confirmed. In a previous version of horae, it > >> worked fine. > >> > > >> >Carlo > >> > > >> > > >> >-- > >> >Carlo U. Segre -- Professor of Physics > >> >Associate Dean for Special Projects, Graduate College Illinois > >> >Institute of Technology > >> >Voice: 312.567.3498 Fax: 312.567.3494 > >> >Carlo.Segre(a)iit.edu http://www.iit.edu/~segre > >> >_______________________________________________ > >> >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 > >> > > > >_______________________________________________ > >Ifeffit mailing list > >Ifeffit(a)millenia.cars.aps.anl.gov > >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > -- > Carlo U. Segre -- Professor of Physics > Associate Dean for Special Projects, Graduate College > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > Carlo.Segre(a)iit.edu http://www.iit.edu/~segre > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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MacOS X 10.3 - Athena Starts...then Stops
by Christopher Derr 11 Jun '04

11 Jun '04

I'm attempting to install Ifeffit 1.25 on a new Powerbook G4 with MacOS X 10.3. I've downloaded the installer (actually I've tried the stable and test versions) and installed into Applications. Clicking on Athena, however, starts Athena (you see the menu at the top change) and then it just goes away. Same with Artemis. Feffit asks for a file to load, but then goes the same route as Athena and Artemis...just goes away. I'll supply more information as needed. It's a brand new laptop with nothing really untoward installed. Thanks for any thoughts whatsoever. Chris

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RE: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Kelly, Shelly D. 11 Jun '04

11 Jun '04

Hi Carlo, Here is something to try. Put all the feffxxxx.dat files into a single directory. Rename them so that you do not have repeating numbers. Then try to read them in all at one time. Shelly > -----Original Message----- > From: Stefano Ciurli [mailto:stefano.ciurli@unibo.it] > Sent: Thursday, June 10, 2004 3:12 PM > To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Artemis: Error in laoding additional > FEFF paths? > > > Carlo, > > I have been having consistent problems running the tutorials on my > MacOSX G4 portable PC. I have posted several times the tect of the > trap files I am getting. .Apparently, there is no definitve answer > (yet). I am sure Bruce will try to clean up things whenever he has > time. But, if for some reason, some of you out there knows a way out, > I'll be one of the many to be happy to read it. > > Stefano. > > >One of my students is just trying Scott's ZnO tutorial and we are > >finding a consistent problem when trying to work with the > third project > >file. > > > >When we get to the point of adding an additional path, > (feff0011.dat), > >artemis crashes with the following message: > > > >--------------------------------- > > > >The following message was trapped by Artemis: > > > >Artemis0.7.006warn/home/segre/.horae/stash/ARTEMIS.TRAPCODE(0 > x9652e54)/ > >home/segre/.horae/stash/artemis.project.2/ > >at /usr/bin/artemis line 1562 > > main::__ANON__('Use of uninitialized value in string eq at > >/usr/bin/artemis l...') called at /usr/bin/artemis line 7313 > > main::read_feff('^^') called at > /usr/lib/perl5/Tk.pm line 225 > > eval {...} called at /usr/lib/perl5/Tk.pm line 225 > > Tk::__ANON__('Tk::Menu=HASH(0x974a060)', 'active') called at > >/usr/lib/perl5/Tk/Menu.pm line 531 > > Tk::Menu::Invoke('Tk::Menu=HASH(0x974a060)', 1) called at > >/usr/lib/perl5/Tk.pm line 347 > > eval {...} called at /usr/lib/perl5/Tk.pm line 347 > > Tk::MainLoop() called at /usr/bin/artemis line 1707 > > > >-------------------------------- > > > >This is happening on all of my Linux machines. They are using my > >Debian packages and so I have not tried with the tarball > installation. > > > >Has anyone else had this problem? I hesitate to report it as a bug > >until it is confirmed. In a previous version of horae, it > worked fine. > > > >Carlo > > > > > >-- > >Carlo U. Segre -- Professor of Physics > >Associate Dean for Special Projects, Graduate College > >Illinois Institute of Technology > >Voice: 312.567.3498 Fax: 312.567.3494 > >Carlo.Segre(a)iit.edu http://www.iit.edu/~segre > >_______________________________________________ > >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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