Re: [Ifeffit] DAthena crashes when reconstructing data from PCA
Hi Scott, I had no problems doing reconstruction of data on two different machines running Windows 8 and DAthena 0.9.17. I used Bruce's gold cyanobacteria example and followed the sequence of operations shown in the PCA section of the Athena Users' Guide (http://bruceravel.github.io/demeter/aug/analysis/pca.html). That would seem to point to something quirky about Parallels. Erik From: Scott Calvin scal...@sarahlawrence.edu To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Wednesday, June 19, 2013 12:07 PM Subject: Re: [Ifeffit] DAthena crashes when reconstructing data from PCA Hi Bruce and Others, I've tried some follow-up troubleshooting. The problem does not occur on another laptop with Windows 7 installed, so it appears to fall under some variation of your possibility #1. I thought perhaps it might be related to some kind of resource problem (e.g. memory allocation), so I played around with giving my Parallels virtual machine various amounts of memory, processing power, etc., but nothing changed the behavior. I would be interested to know from other people on the list if they have gotten the reconstruction of data from PCA to work under Windows 8 (I don't have another Windows 8 machine readily available to test it on). That would help narrow down whether the issue is a general one with that OS, or whether it's something more quirky having to do with the environment I'm using. --Scott Calvin Sarah Lawrence College On Jun 14, 2013, at 9:18 AM, Bruce Ravel bra...@bnl.gov wrote: On 06/11/2013 09:25 PM, Scott Calvin wrote: Athena is crashing every time I try to Reconstruct Data in the PCA dialog. It doesn't seem to matter what data I use, or what space I'm working in (mu or chi), or how many components I use in the reconstruction. I'm using Demeter 0.9.17 with Ifeffit 1.2.11d, under Windows 8 running in Parallels 8 running under OS 10.8.4 on a MacBook Pro. The log file for the latest crash is below. If you'd like a project file too, let me know, but it happens, e.g., with the gold cyanobacteria project file, and with every data set I've tried. Hi Scott, I do not see this behavior on any of my computers (which include native WinXp and Win7 machines and linux) and I am having trouble guessing from the log file you attached a possible cause of the problem. Possibility #1: you are using a configuration that I cannot test. I have never used Parallels and none of my computers are running Windows 8. I'd be surprised if either is the cause of the problem, though. It seems surprising that Athena would get that deeply into its operations before running into a platform-related problem. That said, I'd be interested to know if you see this on a native Win7 or WinXP machine. Possibility #2: you have figured out some combination of mouse clicks and button presses that I have never tested. The problem you are seeing is that the group considered current (i.e. the one that should be the target of the reconstruction) has become unset. Typically, when you click on an item in the group list, Athena will assign that as the current data set. It will then run a simple test to see if it was among the data groups included in the PCA decomposition. If so, the reconstruct button is enabled. If not, the TT button is enabled. I cannot find a compbination of events that leaves me in a state that unsets this, resulting in your stack trace. So without further instruction, I don't know how to go about solving the problem. B ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] demeter windows download
See the Demeter page at http://bruceravel.github.com/demeter/ . Links to the installers can be found on the left panel. Erik From: Darren Dale dsdal...@gmail.com To: ifeffit@millenia.cars.aps.anl.gov Sent: Sunday, February 17, 2013 10:10 AM Subject: [Ifeffit] demeter windows download Hello Bruce, All, I wanted to install Demeter on my windows computer this morning. I followed links to instructions at http://cars9.uchicago.edu/ifeffit/Demeter/WindowsUpdater , which in turns links to https://github.com/bruceravel/demeter/downloads . Unfortunately, github recently discontinued the downloads service, so that is not a functioning link anymore. Is there a new location available to find the installer? Thanks, Darren ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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 efarqu...@bnl.gov +1-631-344-8174 From: Matt Newville newvi...@cars.uchicago.edu To: XAFS Analysis using Ifeffit ifeffit@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 clayt...@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
Re: [Ifeffit] Beryllium and EXAFS
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 mamar...@lbl.gov To: Erik Farquhar ef...@yahoo.com; XAFS Analysis using Ifeffit ifeffit@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 efarqu...@bnl.gov +1-631-344-8174 From: Matt Newville newvi...@cars.uchicago.edu To: XAFS Analysis using Ifeffit ifeffit@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 clayt...@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
Re: [Ifeffit] Fitting pre-edge feature in Fe XANES
Hi Sharon, In addition to Bruce's excellent advice on treating pre-edge analysis as a generic fitting problem, you may also want to have a look at an earlier systematic survey of Fe pre-edge analysis: Westre, et al., J. Am. Chem. Soc. 1997, 119, 6297-6314 DOI: 10.1021/ja964352a. Note the constrained fitting range in that paper, which simplified the fitting problem a bit since they did not need to worry about accurately fitting the edge step and bumps along the rising edge using step functions and the like. The only useful application of EXAFSPAK to your problem would be to fit the pre-edge data using the EDG_FIT program of that package (this was used in the Westre paper referred to above). This program has something of a learning curve to use well. If you have another peak- fitting program that you like, then it's best to stick with that one. Good luck, Erik -- Erik Farquhar, Ph.D. Case Center for Synchrotron Biosciences Brookhaven National Lab NSLS, Building 725A-X3 Upton, NY 11973 efarqu...@bnl.gov +1-631-344-8174 From: shb...@berkeley.edu shb...@berkeley.edu To: ifeffit@millenia.cars.aps.anl.gov Sent: Friday, June 8, 2012 2:18 PM Subject: [Ifeffit] Fitting pre-edge feature in Fe XANES Dear All: I would like to attempt fits to the pre-edge features of a set of Fe K-edge XANES spectra for Fe(II) samples that show partial oxidation with the goal of determining whether Fe(III) exists in octahedral or tetrahedral coordination (e.g. Wilke et al., American Mineralogist, 2001). Broadly, the fitting procedure involves extracting the pre-edge feature from the edge using a spline function and then deconvoluting this feature using a set of pseudo-voigt functions. I believe that I can use the LCF module in Sixpack to fit the feature using the pseudo-voigt functions, but I'm having trouble extracting the pre-edge feature. I've tried using the spline function in Sixpack (and Athena), but I don't have enough options to modify the spline. It seems to me that I need to use a very rigid spline (for instance, one with only 3 or so knots), and that the options in Sixpack and Athena don't allow for this. I heard the program exafspak would allow me more freedom to control the spline function, but I haven't been able to successfully download the program, let alone use it. So, my questions are the following: (1) Is there a program other than exafspak that I could use to fit a spline to my data where I would have more control over the spline options? I would prefer not to use exafspak since my knowledge of unix is nil. (2) Has anyone used exafspak on a mac? I'm using OS 10.5.8 and I'd appreciate any tips you might be able to give me on installing the program. I followed the directions for installation provided on the website, but the command to install the program (i.e. add_exafs) wasn't recognized. Thanks for your help! Sharon ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
