December 2012 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Demeter installation (under Ubuntu)
by Denis Testemale 19 Dec '12

19 Dec '12

Hello Bruce. There are no special characters only letters, numbers, and underscores. To be sure, I tried by placing the athena projects in ~/temp with the same result. Actually, I played a little bit more, and the behaviour is really strange: - consider the home folder /home/denis (I'll write ~ in the following) and a subfolder ~/A - I place an old style athena project in ~: named athena.prj - start dathena - open ~/athena.prj in dathena. It works. - cp athena.prj A/athena.prj - open ~/A/athena.prj in dathena. It works. - rm ~/athena.prj - reopen ~/A/athena.prj in dathena. It says: "/home/denis/athena.prj is not readable" - cp ~/A/athena.prj ~/. - reopen ~/A/athena.prj in dathena. It works. - and finally, I replace ~/A/athena.prj by another athena project (different), i.e., cp ~/some_random_athena_project ~/A/athena.prj - reopen ~/A/athena.prj in dathena. No error message BUT the project it opens is the old one, not the new random one I replaced the original one with... An additional info: the result of this sequence is the same if I let dathena run between each step ((but close the projects CTRL+W) or if I close (CTRL+Q) dathena at every step. What do you think of my Xmas gift Bruce? :-) Cheers denis Le 18/12/2012 19:54, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > ------------------------------ > > Message: 2 > Date: Tue, 18 Dec 2012 13:47:32 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Demeter installation (under Ubuntu) > Message-ID: <3657129.uFgO795gez(a)lachesis.bnl.gov> > Content-Type: text/plain; charset="us-ascii" > > > Hi Denis, > > As always, thanks a million for your feedback. This kind of thing has > a profoundly positive impact on the quality of the package. I am > really grateful. > > The gnuplot-x11 dependency is a good catch. Thanks. > > Unsurprisingly, I have no problems opening files on my computers. So > we need to figure out what is happening on yours that is not happening > on mine. My first suspicion involves character sets. > >> - if I copy athena.prj from /home/denis/pathtothefolder/ to /home/denis/ >> then it works. > What is "pathtofolder"? Specifically does it contains any accented > characters, ess-zets, eastern characters or anything else involving > unicode? > > B > -- Denis Testemale Institut Néel FAME beamline at ESRF +33 476 881 045

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Beryllium XAFS in proteins
by grant bunker 18 Dec '12

18 Dec '12

Gina - measuring Be in proteins is extremely difficult and probably unprecedented, but it may be possible to substitute another element that is chemically similar and probe that instead. For example, often metalloenzymes remain functional under such substitutions, e.g. if you substitute a Mn or a Co in a Ca site. The covalent radius of Be is very small, so substituting Ca might not be feasible without excessively distorting the site, but Aluminum isn't far off, and might work. Of course Aluminum itself isn't easy because of its low k-edge, but it may be feasible. If a heavier element (Ca or heavier) could be made to substitute and retain the functionality/properties you are studying, it might be a suitable probe. good luck! Grant Bunker On Dec 18, 2012, at 3:19 PM, 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: Beryllium and EXAFS (Erik Farquhar) > 2. Larch 0.9.17 available for download and testing (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 18 Dec 2012 12:50:30 -0800 (PST) > From: Erik Farquhar <efarq(a)yahoo.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Beryllium and EXAFS > Message-ID: > <1355863830.4845.YahooMailNeo(a)web141002.mail.bf1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > A bit unrelated to the question at hand, but regarding #5, yes, people do neutron PX.? The focus?is almost entirely on locating hydrogen atoms (e.g. for protonation state), so I wonder what?the neutron PX guys?would say about looking for a Be atom. The downside is that you usually need?quite large crystals compared to X-ray PX and long data collection times. > ? > Erik > > > ________________________________ > From: Matthew Marcus <mamarcus(a)lbl.gov> > To: Erik Farquhar <efarq(a)yahoo.com>; XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Sent: Tuesday, December 18, 2012 1:39 PM > Subject: Re: [Ifeffit] Beryllium and EXAFS > > > Just to stir the pot a little more: > 1.??? ALS has some beamlines which can go down as far as Li.? Work has been done on Li, but only on concentrated stuff. > 2.??? The sample is probably really dilute in Be.? The signal will be pathetic. > 3.??? Radiation damage will be a major issue, especially with X-ray Raman, which is a highly inefficient technique.? Even LHe cooling doesn't solve that problem. > 4.??? Are there model compounds available for proposed local structures of the Be center?? You'd need that to have any hope of making sense out of Be XANES. > 5.??? Is there such a thing as neutron PX?? That might see the Be. > ??? mam > ? > ----- Original Message ----- >> From: Erik Farquhar >> To: XAFS Analysis using Ifeffit >> Sent: Tuesday, December 18, 2012 5:32 AM >> Subject: Re: [Ifeffit] Beryllium and EXAFS >> >> >> To add to Matt's last paragraph, you might also consider beamline 6-2 at SSRL (http://www-ssrl.slac.stanford.edu/beamlines/bl6-2/) as they do a fair amount of work with proteins and have an X-ray Raman setup. I think the beamline scientist occasionally?posts to this list. >> >> >> Good luck, >> Erik >> >> >> -- >> Erik Farquhar, Ph.D. >> Case Center for Synchrotron Biosciences >> Brookhaven National Lab >> NSLS, Building 725A-X3 >> Upton, NY? 11973 >> efarquhar(a)bnl.gov >> +1-631-344-8174 >> >> >> >> ________________________________ >> From: Matt Newville <newville(a)cars.uchicago.edu> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Sent: Tuesday, December 18, 2012 7:52 AM >> Subject: Re: [Ifeffit] Beryllium and EXAFS >> >> Hi Gina, >> >> On Mon, Dec 17, 2012 at 5:23 PM, Clayton, Gina <ClaytonG(a)njhealth.org> wrote: >>> Hi there >>> >>> I am trying to find out more about EXAFS. I am a protein crystallographer. >>> >>> >>> I want to identify the environment of a beryllium ion in the protein, I work with,? of which I have a crystal structure.? EXAFS was recommended as a good technique for identification of the beryllium site and species. The beryllium is an acidic pocket of the protein surrounded by oxygens from the protein, likely covalently bound. However I have had? zero result finding a beam line that can tune their setups to the Be edge at 111 eV. Also some EXAFS users say that EXAFS technique would be good for working out the environment of the Be but some say it would not . In particular? I have been advised that? Be EXAFS would not be useful since? the Be? EXAFS signal would have unacceptable interference from the carbon K-edge at 285 eV and the oxygen K edge signal at 535 eV. >>> >>> Would EXAFS work or something in a similar vein? Or, for instance,? could the acidic pocket be identified using EXAFS, by measuring the oxygens (instead of the Beryllium) using the protein with and without beryllium? >>> >>> >>> Thank you so much for any advice. >>> >>> Gina >> >> As you and as the person who advised you suspect, you face a number of >> challenges: >> >> 1.? The extremely low energy (111 eV).? You might be able to find a UV >> source or x-ray beamline that can reach this energy , but often such >> work is done in vacuo, and so may not be suitable for proteins.? Using >> electrons (from a TEM, say) might be possible too -- these can >> sometimes do C and N edges either directly or looking at Electron >> Energy Loss (send in an electron of high energy E1, and look for >> electrons of energy E1 - E, and scan the analyzer for the loss energy >> E through the absorption edge).? Again, electron probes may not be >> what you want for your proteins. >> >> 2. The C K-edge will limit your signal to "only" 175 eV.? I would say >> to not worry so much about this limitation.? You'll really be >> measuring NEXAFS (near-edge X-ray absorption ....)? but that's OK. >> People measure the B, C, N, and O K edges, all facing the same >> problem, especially for the O K edge: our planet is more or less >> covered with the stuff ;).? These spectra tend to be very rich and >> sensitive to ligands. >> >> 3. Not much (zero?? I can almost believe that!) literature on Be XAFS. >> This is unfortunate because most NEXAFS is measure and compare to >> known spectra.? I think that might mean you have to spend effort to >> building up a spectral library for Be in organic phases. >> >> I think trying to measure the O K edge with and without Be is nearly >> hopeless.? All the X-ray spectroscopies average equally over all the >> atoms of the absorbing species.? In addition all the spectra are >> grossly the same (a step function from 0 below the edge to 1 above the >> edge).? These make it difficult to see changes below about 1%.? ? So I >> think you would just have too high of an O::Be ratio to see anything >> useful. >> >> One option to consider is using X-ray Raman scattering >> (http://en.wikipedia.org/wiki/X-ray_Raman_scattering).? Here, one hits >> the sample with high-energy X-rays (say, 10 keV), which are highly >> penetrating for reasonably sized protein sample.? One analyzes an >> energy loss (again, E1 - E, where here E1 is around 10 keV) to get the >> edge of interest.? I'm familiar with (been involved with) studies on >> B, C, and O using this technique (all in solids, mostly at high >> pressure).? See, for example,? S. K. Lee, et al "Probing of bonding >> changes in B2O3 glasses at high pressure with inelastic X-ray >> scattering",? Nature Materials 4, pp 851-854 (2005), and also the work >> of Simo Huotari.? ? I'm not aware of anyone doing Be K-edge this way, >> but it should definitely be possible. For the work I've been involved >> with, Be would be challenging because there are other excitations in >> solids that appear around 100 eV.? I believe that effect would be far >> suppressed in a protein, though I'm not sure. >> >> That's somewhat more exotic than straightfoward XAFS,, but it might be >> the best chance for measuring Be in a protein.? ? I'm not sure I know >> any beamlines that do X-ray Raman on proteins, but I'd suggest APS >> beamline 20-ID or ESRF beamline as places to start.? ? The next >> questions would be "how many Be atoms are in your protein?", and "how >> much material do you have?".... >> >> Hope that helps, >> >> --Matt Newville >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> >> >> ________________________________ >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >

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Beryllium and EXAFS
by Clayton, Gina 18 Dec '12

18 Dec '12

Hi there I am trying to find out more about EXAFS. I am a protein crystallographer. I want to identify the environment of a beryllium ion in the protein, I work with, of which I have a crystal structure. EXAFS was recommended as a good technique for identification of the beryllium site and species. The beryllium is an acidic pocket of the protein surrounded by oxygens from the protein, likely covalently bound. However I have had zero result finding a beam line that can tune their setups to the Be edge at 111 eV. Also some EXAFS users say that EXAFS technique would be good for working out the environment of the Be but some say it would not . In particular I have been advised that Be EXAFS would not be useful since the Be EXAFS signal would have unacceptable interference from the carbon K-edge at 285 eV and the oxygen K edge signal at 535 eV. Would EXAFS work or something in a similar vein? Or, for instance, could the acidic pocket be identified using EXAFS, by measuring the oxygens (instead of the Beryllium) using the protein with and without beryllium? Thank you so much for any advice. Gina NOTICE: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.

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plotting backends in Demeter
by Bruce Ravel 18 Dec '12

18 Dec '12

Hi, This afternoon I noticed that someone who goes by the handle "khuonggit" posted a question at David Hughes' gist about installing Demeter on Ubuntu. https://gist.github.com/3959252 I hope he is reading this mailing list. khuonggit asked: I am beginner in EXAFS. I tried to install Demeter in Ubuntu 12.04 64 bit following the guidance here and the installation was successful. However, when I tried to open (d)athena and import some data, the default plotting backend is PGPLOT, not GNUPLOT. Could you please show me how to change it to GNUPLOT ? Good question. In the time since khuonggit posted that question, I have modified the build script to attempt to detect the presence of gnuplot and modify Demeter's configuration accordingly. Hopefully, this will become a non-issue in the future. The plotting backend can be set by hand at any time in any of the GUI programs by editing the preferences. In Athena, choose "Preferences" from the main menu. In Artemis, choose "Edit preferences" from the file menu. In Hephaestus, click on the Configure icon at the bottom left. Once at the preferences tool, select "Plot" then "plotwith". Select "gnuplot" then click "Apply and save". B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Re: [Ifeffit] How to do with diffraction peak
by Matt Newville 15 Dec '12

15 Dec '12

Hi Matthew, On Wed, 12 Dec 2012, Matthew Marcus wrote: > > On 12/12/2012 8:03 PM, Matt Newville wrote: >> Hi Matthew, Bruce, All, >> >> Sorry for not being able to join this discussion earlier. I agree >> that having glitch-free data is preferred. But I also think it's OK to >> simply remove diffraction peaks from XAFS data -- you're just >> asserting that you know those values are not good measurements of >> mu(E). I don't see it as all that different from removing obvious >> outliers from fluorescence channels from a multi-element detector -- >> though that has the appeal of keeping good measurements at a >> particular energy. > > That's kind of my point. The standard methods, which require uniform > tabulation, cause you to fill gaps in data by interpolation. > Effectively, you're claiming knowledge of data for which you don't have > knowledge. Better to use a method which preserves > agnosticism about the bad data. The method I described for deglitching with > reference scalers tries to preserve what information > you do have by allowing you to ignore some channels. That only works if > there are 'good' channels to serve as references. I would say that identifying a point as an invalid measure of mu(E) and simply not excluding it in the analysis is OK: it is claiming knowledge that we didn't measure that point well. I just don't see it as much different from claiming that outliers in the set of fluorescence intensities are not good measures of fluorescence intensity. You might argue (I would agree) that with multiple measures of fluorescence you can determine outliers more rigorously. But I would also say that then the best thing to do then is to not simply remove outliers but to take the average AND standard deviation of the samples and include both in the analysis. A glitch would then not be removed, but would be reflected by having a less certain value for that energy point. >> I'm not sure that "slow FT" versus "discrete FT" is that important >> here, though perhaps I'm missing your meaning. My vies is that The >> EXAFS signal is band-limited (finite k range due to F(k) and 1/k, and >> finite R range due to F(k), lambda(k), and 1/R^2), so that sampling >> on reasonably fine grids is going to preserve all the information that >> is really there. > > Again, FFT requires a uniform tabulation of data in k-space, which is > generally secured by interpolation. Traditionally, this has > been histogram interpolation, which tries to take into account the > possibility of having multiple data points within one of the new > intervals in k. That method, however, has to 'make up' data when there isn't > any in one or more intervals. > > Actually, there are three possible tiers of speed. There's FFT, there's > discrete FT done the slow way by computing the sums as > they appear in the textbook (possibly good if you want a funny grid in R > space), and then there's what I propose. I agree with your larger point that we can definitely afford the CPU cycles to do better analysis than use something simply because it is Fast. I'm not sure that a slow discrete FT would be significantly different than an FFT, though. I think (but am listening...) that the continuous v discrete FT is like classic audiophile snobbery about the superiority of analog over digital music. With sufficient sampling and resolution and dynamic range in the signal, the difference has to be trivial. I'm willing to believe that a digital recording has less dynamic range, but I'm also willing to believe that this is swamped by my stereo and ears (and I mostly listen to mp3s through cheap headphones these days, so I clearly am not buying a tube amplifier anytime soon...). But for EXAFS, we know the limits of the signals in k and R (say, 50 Ang^-1 and 25 Ang for extrema), and so can choose samplings that definitely over-sample enough to not cause significant artifacts. There can be dynamic range issues (especially with standard pre-amplifiers and VtoF converters), but I think this is a slightly separate issue from "the glitch problem". Interpolation methods are definitely worth discussing and studying. I'm not sure that the energy values that happened to have been where the monochromator was stopped for a measurement of mu(E) are more sacred or a better sampling of the first shell of an EXAFS spectra than a set of energies interpolated from those measurements to be on uniform k grid, provided the the original data isn't woefully undersampled. With a typical step size of 0.05Ang^1 you can easily miss several points and still accurately measure distances up to 5 or probably even 10 Angstroms. >> I do think that having richer window functions and spectral weightings >> would be very useful. You could view chi(k) data with glitches ias >> wanting a window function that had a very small value (possibly zero: >> remove this point) exactly at the glitch, but had a large value (~1) >> at nearby k-values. >> >> Another (and possibly best) approach is to assign an uncertainty to >> each k value of chi. At the glitch, the uncertainty needs to go way >> up, so that not matching that point does not harm the overall fit. > > A window function which went to 0 in the glitch region is tantamount to an > assertion that chi(k)=0 there, which is generally not so > and is probably a lot worse than the error you make by even the lamest > interpolation through the glitch. The uncertainty makes more > sense, except that if you filter data, the noise spreads out in a correlated > manner over adjacent regions. Also, the tacit assumption > of an uncertainty-based method is that the noise is uncorrelated within the > high-uncertainty region. That said, I can imagine that > this is one of those methods that works better than it has any right to. I think of the window as weighting of measurements to consider, and that a weight of zero is applied to data with infinite uncertainty. I don't think of chi(k) as zero outside the window range (say, below kmin or above kmax), just that we don't want to consider that in the analysis. Again, I think the better thing would be to have an uncertainty for each value of chi(k), and propagate that through the analysis. > Now, in my proposed system, how would you fit filtered (q-space) data? The > first step is to do the very slow FT (VSFT) on the input > data with no interpolation. This leads to a set of sines and cosines which > replicate the data. I would then apply the window and > do the back-summation of all those sines and cosines at the given points. > This will undoubtedly introduce some artifacts near > the edges of the deleted regions simply due to our ignorance of what the data > really do in there. Next, in each fit iteration, I would > evaluate the model function at each point, then do the VSFT and filtering > exactly as had been done on the data, which causes the fit to > have the same artifacts. Since the VSFT and filter operations are linear, it > should be possible to pre-compute a kernel which relates the > values of unfiltered data to those of filtered data. This would be a matrix > of size Np*Np with Np=# of points. Using the kernel instead > of evaluating gazillions of trig functions would be reasonably fast; I > suspect that ifeffit does a similar trick. Similarly, fitting in > R-space would be accomplished by computing the VSFT on data and model > function. > > Yes, I know I talk a good game. Unfortunately, I'm too swamped to attempt > implementation. Also, I'd have to reinvent a number of > very well-engineered wheels to do it. I hear you! I'm interested in pursuing "more advanced weightings and transforms", but don't have much time to spend on such things these days, so development is slow.... >> Larch has a separate Transform class used for each dataset in a fit - >> this includes the standard FT parameters and fit ranges. It is >> intended to be able to do this sort of advanced windowing (and in >> principle, advanced weighting too). Currently (I'd be ready for a >> release but am commissioning our new beamline and am hoping to post a >> windows installer by the end of the month) this has "the standard >> XAFS window functions", but one can create their own window functions >> (for k- and/or R-space) with suppressed points/regions, etc, and use >> them as well. I have to admit I haven't tried this, but it was >> definitely part of the intention, and should work. My hope is to >> extend this to include some wavelet-like weightings as well. >> > What is Larch? Is it a replacement for ifeffit? By 'class' do you mean > object as in OOP? > "And now for something completely different. The larch." - Monty Python > mam Yes, Mostly yes, and, Yes, you get the reference exactly ("How to recognize different types of trees from quite a long way away, Number 1: The Larch"). http://xraypy.github.com/xraylarch/ Another wide-open appeal: I'd love help in implementing improvements like these (better windows, comparing continuous v discrete transforms, using wavelets, etc), and think work like this would be publishable. There are several other improvements I'd like to see, such as generating Feff Paths on-the-fly, and so forth. Essentially all of Larch is in python so that it's very easy to modify and add features like this. The available numerical libraries for python are plentiful and well-maintained. It's also easy to add wrappers for C and Fortran code if that is needed..... --Matt

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merging data
by George Sterbinsky 14 Dec '12

14 Dec '12

Hello, I am observing some behavior in (D)Athena that I do not understand, and I was hoping someone could explain it to me. I have attached a project file to illustrate my question. The first two groups in the file have been normalized such that mu(E) and norm(E) are identical. I then merged these groups in mu(E) and norm(E), also in the file. Since mu(E) and norm(E) are the same for the groups, I would expect the data merged in mu(E) and norm(E) to also be identical, but it is not. While it is clear that merging in mu(E) is averaging the groups, it seems merging in norm(E) is not. So what is merging in norm(E) doing? Thank you, George

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How to do with diffraction peak
by Zhaomo Tian 13 Dec '12

13 Dec '12

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Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 13
by jiahui 12 Dec '12

12 Dec '12

Hi Bruce, Thank you very much for the effort. jiahui -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 12 December 2012 22:17 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 118, Issue 13 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: How to do with diffraction peak (Bruce Ravel) 2. Re: How to do with diffraction peak (Anatoly I Frenkel) 3. Re: Ifeffit Digest, Vol 118, Issue 6 (Bruce Ravel) 4. Re: How to do with diffraction peak (Dr. Dariusz A. Zaj?c) 5. Re: How to do with diffraction peak (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 12 Dec 2012 13:03:46 -0500 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] How to do with diffraction peak Message-ID: <8927581.5aRJTKJtsK(a)lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" On Wednesday, December 12, 2012 09:49:45 AM Matthew Marcus wrote: > Here's one last trick that I used to use when I used a plastic > scintillator at NSLS and didn't have a spinner. WARNING - this is > painful! I used to tape a piece of Polaroid film to the face of the > detector, run through a scan, develop the film, see where the white > spots were, and put Pb tape on the detector at those spots. Told you it was painful! These days, I suspect the painful part is *finding* polaroid film! :) B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel ------------------------------ Message: 2 Date: Wed, 12 Dec 2012 18:04:00 +0000 From: Anatoly I Frenkel <afrenke2(a)yu.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] How to do with diffraction peak Message-ID: <545F89325F51764C902D37B42C9F4D531363A77F(a)YUWEXCPM12.yuad.uds.yu.edu> Content-Type: text/plain; charset="iso-8859-7" (For masochists only): I still have Matthew's plastic scintillator in my cabinet at the NSLS, so if anyone is willing to try this trick with the original hardware, let me know. Anatoly ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of Matthew Marcus [mamarcus(a)lbl.gov] Sent: Wednesday, December 12, 2012 12:49 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] How to do with diffraction peak Here's one last trick that I used to use when I used a plastic scintillator at NSLS and didn't have a spinner. WARNING - this is painful! I used to tape a piece of Polaroid film to the face of the detector, run through a scan, develop the film, see where the white spots were, and put Pb tape on the detector at those spots. Told you it was painful! Aside from that, I think Bruce is right - you're screwed with 1-channel data, especially if the Bragg peaks are broad and/or come in the XANES region. If you have to take data without a spinner or multi-element detector, the trial-and-error method of changing the sample orientation often works to shift the Bragg peaks away from sensitive parts of the spectrum to where you don't mind too much losing some points. I have never tried fitting peak shapes to the Bragg peaks (say, a Lorentzian or pseudo-Voight plus a smooth polynomial; don't subtract the polynomial). I suspect that the peak shapes aren't 'nice' enough for that to work reliably. The shapes of the tails, for instance, would be influenced by the angular divergence of the beam onto the sample and into the monochromator and any strain. mam On 12/12/2012 7:28 AM, Bruce Ravel wrote: > On Tuesday, December 11, 2012 04:08:03 PM Zhaomo Tian wrote: >> I got XAFS data for Ag with CO adsorption( using Ag K edge), Ag is >> thin film~300nm deposited on Si/SiO2 substrate. But in the original >> ?(E) spectra, from 25894-26044eV, four obvious diffraction peaks >> appear( I attached the file), and I guess they will influence the quality of fitting. >> Is there anyone who knows how to deal with these diffraction peak? >> Will it be corrected by smoothing or changing some origin data points >> in the original file? I want the modification that will not destroy >> data analysis later. > > You have received some decent advice on how to post-process your data > to minimize the effect of the diffraction peak. I think it bears > mentioning that not all prblems are best solved after the fact in > software. Some problems should be addressed as the data are measured > or even beforehand. > > I see from the data file you sent that you were at beamline 10C at > Pohang. It is hard to tell for certain from the data file or from the > website, but it seems as though you were using a PIPS detector to > measure your fluorescence XAFS. > > This is an experimental setup can be a difficult one to combine with a > sample that diffracts. The sort of PIPS commonly used at an XAS > beamline tends to be of a very large surface area. That means that > the likelihood of some diffraction peak from the sample hitting the > detector during the measurement is pretty high. In fact, it happened > 4 times for you. That means you have a lot of data points to > deglitch, were you to follow Kicaj's advice. Because you used a PIPS > rather than a multi-element detector, you don't have the option of > following any of Matthew's (excellent) advice. > > I hate to say it, but I think you are screwed. The best you can do is > deglitch as best you can. Because you will be removing so many points > from the data, you will introduce substantial systematic error into > the data set that remains. I don't really see what you can do about > that at this late date. > > So, what might you do the next time you visit the synchrotron to > obtain better data? In fact, there are number of things that you can > consider at the stages of sample preparation or of data collection. > > 1. You don't say a lot about the sample or its substrate. Perhaps you > have a reason that the substrate *must* be crystalline. Perhaps > not. Putting your film on an amorphous substrate would obviate the > problem of diffraction from the substrate. That may be your best > bet. > > 2. The large size of the PIPS detector is a contributing factor to the > problem. Simply using a detector with a smaller surface area > reduces (but certainly does not eliminate!) the likelihood of > diffraction peaks hiiting it. Moving the detector farther away > from the sample would serve the same purpose. Of course, doing so > would also serve to reduce your count rate, thus reducing the > quality of your data. There is a cost to everything! > > 3. Use the 13 element Ge detector instead of the PIPS. Then you can > simply eliminate channels hit by Bragg peaks or do the > post-processing trick Matthew described. > > 4. At my beamline, we have users almost every cycle who measure stuff > on crystalline substrates. Our favorite trick is to mount the > sample on a spinner (e.g. http://dx.doi.org/10.1063/1.1147815) At > my beamline, we actually attach the sample the sort of small DC fan > that is used to cool electronics. Inexpensive, simple, and > effective! By keeping the sample constantly in motion, the energy > at which the Bragg condition is met is constantly changing. This > serves to reduce the effect of the Bragg peak by a few orders of > magnitude by spreading it out in energy. Usually, it can be made > smaller than chi(k), resulting in analyzable data. > > The bottom line is that you have the sort of problem that I think > needs to be solved up front rather than after the fact. > > I know that's not helpful right now, but hopefully it will be the next > time you go to the beamline. > > Cheers, > B > > > _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ------------------------------ Message: 3 Date: Wed, 12 Dec 2012 13:53:23 -0500 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 6 Message-ID: <2296463.dEQb5rDBsc(a)lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" Jiahui, Thanks again for the bug report. Your CIF file exposed a rather subtle bug in the code that parses CIF files. It will be fixed in the next release -- hopefully before the end of the month. Cheers, B On Monday, December 10, 2012 11:16:14 PM jiahui wrote: > Hi Bruce, > > I am a windows user. The two log file(Artemis and Atoms) and one of > the CIF files I used are attached to this email. Please let me know if > you need more information, > > > > Hi Dan, > > I use Mercury to open the CIF file then save as another CIF file as > you suggested. The new CIF file can be read by (D)Artemis with an > warning message basically says there're some problem with this file > and some possible ways to solve the problem(s). > > I actually went to download an old version of IFEFFIT: Ifeffit 1.2.11. > This version can read the CIF files. I ran atoms and FIFF on it. Then > save the file. It could be opened by (D)Artemis without problem. > > Thank you very much for your help and solutions, > > > Jiahui > > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of > ifeffit-request(a)millenia.cars.aps.anl.gov > Sent: 10 December 2012 18:00 > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 118, Issue 6 > > 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. Help: Artemis closes without error message when open .cif > file (jiahui) > 2. Re: Help: Artemis closes without error message when open .cif > file (Bruce Ravel) > 3. Re: Help: Artemis closes without error message when open.cif > file (Daniel Whittaker) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 10 Dec 2012 15:42:27 -0000 > From: "jiahui" <qijiahui.uk(a)gmail.com> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Help: Artemis closes without error message when > open .cif file > Message-ID: <50c602e5.424cb40a.0dd5.42e3(a)mx.google.com> > Content-Type: text/plain; charset="us-ascii" > > Dear list, > > I am having this problem when I try to open the crystal structure file > in .cif format. I've tried many times already--each time when I try to > open the crystal structure file in *.cif format, both (D)Atoms and > (D)Artemis will close by themselves without any error message. > What can I do to solve this problem and carry on with my work? I am > using Demeter 0.9.13 version. > > Thank you very much for your help, > > [jiahui] > > > > ------------------------------ > > Message: 2 > Date: Mon, 10 Dec 2012 10:48:21 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Help: Artemis closes without error message when > open .cif file > Message-ID: <61620056.C2dlAnbQpv(a)lachesis.bnl.gov> > Content-Type: text/plain; charset="us-ascii" > > > Jiahui, > > It would be helpful to me to see an example of a CIF file that > triggers this problem. If you are running on Windows, then I would > also like to see the contents of the %APPDATA%\demeter\dartemis.log > file. See > > http://bruceravel.github.com/demeter/pods/bugs.pod.html > > If you are a linux user, I would need to see the messages sent to the > terminal, which requires running the program from the terminal rather > from some launcher widget. > > As I have said many times before on this mailing list, CIF support is > rather weak at this time. I am using a CIF parsing tool written by > someone else and it has its problems. That said, as people report > these problems, I am able to build more smarts into Demeter so that it > at least deals gracefully with a CIF file it doesn't understand. > > Cheers, > B > > On Monday, December 10, 2012 03:42:27 PM jiahui wrote: > > Dear list, > > > > I am having this problem when I try to open the crystal structure > > file in .cif format. I've tried many times already--each time when I > > try to open the crystal structure file in *.cif format, both > > (D)Atoms and (D)Artemis will close by themselves without any error message. > > What can I do to solve this problem and carry on with my work? I am > > using Demeter 0.9.13 version. > > > > Thank you very much for your help, > > > > [jiahui] > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > Dear list, > > > > I am having this problem when I try to open the crystal structure > > file in .cif format. I've tried many times already--each time when I > > try to open the crystal structure file in *.cif format, both > > (D)Atoms and (D)Artemis will close by themselves without any error message. > > What can I do to solve this problem and carry on with my work? I am > > using Demeter 0.9.13 version. > > > > Thank you very much for your help, > > > > [jiahui] > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel ------------------------------ Message: 4 Date: Wed, 12 Dec 2012 23:09:29 +0100 From: "Dr. Dariusz A. Zaj?c" <kicaj(a)ifj.edu.pl> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] How to do with diffraction peak Message-ID: <50C90099.902(a)ifj.edu.pl> Content-Type: text/plain; charset=UTF-8; format=flowed W dniu 12-12-12 18:49, Matthew Marcus pisze: > I have never tried fitting peak shapes to the Bragg peaks (say, a > Lorentzian or pseudo-Voight plus a smooth polynomial; don't subtract > the polynomial). I have never tried too, simply I took care of data during experiment, as is mentioned in posts before. And I suppose it would be very painful, more than Pb tape... Anyway - good ideal with this Pb tape. coming back to the problem with Bragg peaks, does anyone knows if it is possible to analyse EXAFS with more than 1 interest regions? like 2 or more FT windows - before, between and after Bragg peaks, or is possible to introduce one own FT window function in Athena? regards kicaj ------------------------------ Message: 5 Date: Wed, 12 Dec 2012 17:16:35 -0500 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] How to do with diffraction peak Message-ID: <1733074.77ouYmhRdV(a)lachesis.bnl.gov> Content-Type: text/plain; charset="utf-8" On Wednesday, December 12, 2012 11:09:29 PM Dr. Dariusz A. Zaj?c wrote: > coming back to the problem with Bragg peaks, does anyone knows if it > is possible to analyse EXAFS with more than 1 interest regions? like 2 > or more FT windows - before, between and after Bragg peaks, or is > possible to introduce one own FT window function in Athena? Interesting question. Some days I really love this mailing list. A similar question came up recently on the mailing list, although I think here you are asking whether regions can be chosen in k-space. (The previous discussion was about regions in R space.) I am commenting off the top of my head here, so I may be neglecting something. But I think what you are suggesting to have a windowing function that goes up, then down, then up again, then down again. I think the problem with that is that it would introduce low frequency components into the transformed data. Granted, the transform of the theory would have the same effect, but I worry about how that kind of windowing function would be correlated with the parameters of the fit. As Scott suggested in the earlier conversation, another option is to do a multiple data set fit where the data is imported twice. For one instance of the data, the FT window is set over the first range. For the other instance, the window is set over the second range. Again, I worry about how the choice of windows may be correlated with the parameters of the fit, given the limited information content used in each part of the MDS fit. I don't plan on exploring this myself. But if someone wanted to do so and attempt to convince me that it should be implemented in the software, I am -- as always -- willing to listen. Cheers, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 118, Issue 13 ****************************************

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Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 6
by jiahui 12 Dec '12

12 Dec '12

Hi Bruce, I am a windows user. The two log file(Artemis and Atoms) and one of the CIF files I used are attached to this email. Please let me know if you need more information, Hi Dan, I use Mercury to open the CIF file then save as another CIF file as you suggested. The new CIF file can be read by (D)Artemis with an warning message basically says there're some problem with this file and some possible ways to solve the problem(s). I actually went to download an old version of IFEFFIT: Ifeffit 1.2.11. This version can read the CIF files. I ran atoms and FIFF on it. Then save the file. It could be opened by (D)Artemis without problem. Thank you very much for your help and solutions, Jiahui -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 10 December 2012 18:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 118, Issue 6 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. Help: Artemis closes without error message when open .cif file (jiahui) 2. Re: Help: Artemis closes without error message when open .cif file (Bruce Ravel) 3. Re: Help: Artemis closes without error message when open.cif file (Daniel Whittaker) ---------------------------------------------------------------------- Message: 1 Date: Mon, 10 Dec 2012 15:42:27 -0000 From: "jiahui" <qijiahui.uk(a)gmail.com> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Help: Artemis closes without error message when open .cif file Message-ID: <50c602e5.424cb40a.0dd5.42e3(a)mx.google.com> Content-Type: text/plain; charset="us-ascii" Dear list, I am having this problem when I try to open the crystal structure file in .cif format. I've tried many times already--each time when I try to open the crystal structure file in *.cif format, both (D)Atoms and (D)Artemis will close by themselves without any error message. What can I do to solve this problem and carry on with my work? I am using Demeter 0.9.13 version. Thank you very much for your help, [jiahui] ------------------------------ Message: 2 Date: Mon, 10 Dec 2012 10:48:21 -0500 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Help: Artemis closes without error message when open .cif file Message-ID: <61620056.C2dlAnbQpv(a)lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" Jiahui, It would be helpful to me to see an example of a CIF file that triggers this problem. If you are running on Windows, then I would also like to see the contents of the %APPDATA%\demeter\dartemis.log file. See http://bruceravel.github.com/demeter/pods/bugs.pod.html If you are a linux user, I would need to see the messages sent to the terminal, which requires running the program from the terminal rather from some launcher widget. As I have said many times before on this mailing list, CIF support is rather weak at this time. I am using a CIF parsing tool written by someone else and it has its problems. That said, as people report these problems, I am able to build more smarts into Demeter so that it at least deals gracefully with a CIF file it doesn't understand. Cheers, B On Monday, December 10, 2012 03:42:27 PM jiahui wrote: > Dear list, > > I am having this problem when I try to open the crystal structure file > in .cif format. I've tried many times already--each time when I try to > open the crystal structure file in *.cif format, both (D)Atoms and > (D)Artemis will close by themselves without any error message. > What can I do to solve this problem and carry on with my work? I am > using Demeter 0.9.13 version. > > Thank you very much for your help, > > [jiahui] > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel ------------------------------ Message: 3 Date: Mon, 10 Dec 2012 16:16:00 -0000 From: "Daniel Whittaker" <daniel.whittaker(a)postgrad.manchester.ac.uk> To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Help: Artemis closes without error message when open.cif file Message-ID: <6229BE20E02F4353A75ACA302F4B84CD@mbdx5dw2PC> Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Hi Jiahui, I have experienced similar issues with cif files - there are so many slightly different formats. I found a solution was to open the file in Mercury: http://www.ccdc.cam.ac.uk/free_services/mercury/downloads/ Save it as a .cif from within the program itself and then read it into (D)Artemis. If that works then brilliant :) - If not then there are a few other issues I have found working on my organic systems: 1) If there is any disorder I find it best to remove it. 2) When running atoms I have found it can produce an error. In this case, if you save the file it produces (*.inp) then open this in a text editor and remove any duplicate atoms (normally near the bottom of the file) save it again and then reopen in Atoms then it should work fine. I hope this helps troubleshoot your issues for now? Regards, Dan Daniel Whittaker, MChem Nuclear FiRST DTC PhD Student Chemistry Building The University of Manchester Brunswick Street Manchester M13 9PL -----Original Message----- From: Bruce Ravel Sent: Monday, December 10, 2012 3:48 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Help: Artemis closes without error message when open.cif file Jiahui, It would be helpful to me to see an example of a CIF file that triggers this problem. If you are running on Windows, then I would also like to see the contents of the %APPDATA%\demeter\dartemis.log file. See http://bruceravel.github.com/demeter/pods/bugs.pod.html If you are a linux user, I would need to see the messages sent to the terminal, which requires running the program from the terminal rather from some launcher widget. As I have said many times before on this mailing list, CIF support is rather weak at this time. I am using a CIF parsing tool written by someone else and it has its problems. That said, as people report these problems, I am able to build more smarts into Demeter so that it at least deals gracefully with a CIF file it doesn't understand. Cheers, B On Monday, December 10, 2012 03:42:27 PM jiahui wrote: > Dear list, > > I am having this problem when I try to open the crystal structure file > in .cif format. I've tried many times already--each time when I try to > open the crystal structure file in *.cif format, both (D)Atoms and > (D)Artemis will close by themselves without any error message. > What can I do to solve this problem and carry on with my work? I am > using Demeter 0.9.13 version. > > Thank you very much for your help, > > [jiahui] > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 118, Issue 6 ***************************************

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How to do with diffraction peak
by Zhaomo Tian 12 Dec '12

12 Dec '12

1 0