July 2005 - Ifeffit - millenia.cars.aps.anl.gov

RE: [Ifeffit] A question
by Frenkel, Anatoly 11 Jul '05

11 Jul '05

.... and if you use SS and OVERLAP cards in FEFF, use Bohr's units, which is cute but I hope they will convert this units to Angstroms some day. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Scott Calvin Sent: Monday, July 11, 2005 2:25 PM To: XAFS Analysis using Ifeffit Cc: SCalvin(a)slc.edu Subject: Re: [Ifeffit] A question At 11:45 AM 7/11/2005 -0500, Bruce wrote: >On Monday 11 July 2005 10:39, Mark Mark wrote: >> Hi >> Thank you all for the help. I wonder if I have to use X,Y, and Z parameters >> while originating a feff input file from ATOM or I can use X/a, Y/b, and >> Z/c parameters. I appreciate all the help. > >I don't quite understand the question, but perhaps an example of an >atoms input file would help clarify. This is taken from the examples >that come with the software: >> I would add to Bruce's comment that the FEFF.INP file then gives coords in terms of angstroms, rather than the cell coordinates ATOMS uses. So if you create or modify a FEFF.INP file directly, use angstroms. For an ATOM.INP file use cell coordinates. --Scott Calvin Sarah Lawrence College _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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A question
by Mark Mark 11 Jul '05

11 Jul '05

Hi Thank you all for the help. I wonder if I have to use X,Y, and Z parameters while originating a feff input file from ATOM or I can use X/a, Y/b, and Z/c parameters. I appreciate all the help. Mark __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Missing ipot problem
by rvv052＠mail.usask.ca 09 Jul '05

09 Jul '05

I was able to fix the problem with too many atoms, but then I get another error. It says: No atoms or overlap cards for unique pot 1 Cannot calculate potentials, etc. I know that this problem occurs because potentials 0, 2, 3, 4, 5, and 7 exist in the ipot coloumn, but I do not have a 1 potential (or a 6 potential as I found out by assigning a 1 potential to one of the other atoms). I never encountered this problem with ifeffit during my other calculations, so I am wondering what it means and what I can do about it. Remko van den Hurk

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Exit wavefunctions as f(incoming planewave)
by Schiros, Theanne 07 Jul '05

07 Jul '05

Hello- I'm forwarding a question from a colleague outside the EXAFS community for which I don't have a good answer in hopes that some of you will... "Thinking about EXAFS, I was recently involved in an attempt to analyse TEM images. There are now effective ways to get the complete exit electronic vawefunction as a function of the incoming planewave. It would be quite interesting to be able to get the atomic potentials from the plane wave. This seems to me an inverse problem quite similar to that of the EXAFS you are working on. Do you know of any attempt in that direction? Do you think the softwares you use for solving EXAFS could be used/adapted in this way?" Thanks! theanne

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RE: [Ifeffit] R-factor
by Frenkel, Anatoly 06 Jul '05

06 Jul '05

Victor raised a very good point. To extend his suggestion, I would find the best fit parameters by fitting the original data. Then, I would fit the back-Fourier-transformed data in the same exactly r-range as before, using the same q-range as the k-range used in the first fit. All fit parameters should be fixed to the best fit values found earlier and run the "fit" again (nothing is going to be varied). This will assure that you are varying only one factor in this comparison: the spectral content. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of vikrai(a)comcast.net Sent: Wed 7/6/2005 12:22 PM To: XAFS Analysis using Ifeffit Cc: Subject: Re: [Ifeffit] R-factor Alison, I don't think that the difference of R-factors you mention is a big deal. You did not mention in your message more important thing. Did you get the same values of parameters? Besides, it is hardly to expect to find a signal caused by photoelectron backscattering at R<1 A. So the lower limit in R-space fitting equal to 0.1 A is too small probably. As well as the lower limit in q-space fitting because in proteins in this momentum region only full multiple scattering approach should work correct. Victor Krayzman -------------- Original message -------------- > Bruce, > > I've looked, and my R-factors for the back-transformed > space are not necessarily twice the value of the R-factors > for the k-space fits. In fact, they are often quite > close. For example, just recently I had a k-space > R-factor of 0.102 and a q-space R-factor of 0.113. Now, I > realize those numbers are very close, but I'm afraid if I > try to publish this, then I will get criticism for the > q-space R-factors being larger. If I can explain it, then > maybe it won't be a problem. > > I do see what you're saying about the complex vs. real > function, and that definately makes sense, but they don't > differ by a factor of 2. Hmmm. > > alison > > On Wed, 6 Jul 2005 09:43:03 -0500 > Bruc! e Ravel wrote: > > On Tuesday 05 July 2005 18:39, Alison Costello wrote: > >> I have a question regarding the calculation of the > >>R-factor. I am > >> currently using SIXPACK to process my protein EXAFS > >>data, and I fit the > >> data in both k-space and in q-space (back-transformed > >>k-space). I > >> typically will use k-ranges = [1-13.6] and for > >>multiple-scattering fits, > >> will use an R-range of 0.1 - 4.5. Sometimes, the > >>R-factor for the q-space > >> fit is greater than the R-factor for the k-space fit, > >>which should not be > >> true, as the back-transformed space filters out noise. > >> I am confused as to > >> why this occurs, and am wondering if the R-factor for > >>the back-transformed > >> space is calculated differently than for k-space f! its. > > > > A lison, > > > > I would expect the R factor to be bigger in k space due > >to the high frequency > > portions of the data that get filtered out of the q > >space data. That is what > > happened in the one example I just tried. > > > > What are some example values of the R-factors? Do they > >differ by about a > > factor of 2? > > > > One thing that occurs to me is that chi(q) is a complex > >function while chi(k) > > is a real function. In Ifeffit those two functions > >should have the same > > number of points, but the R factor in q is computed > >using both parts of the > > complex function. Thus it would seem reasonable if they > >differed by about 2 > > and there were no significant Fourier components in the > >data beyond your rmax. > > > > B > > > > -- & gt; > Bruce Ravel ----------------------------------- > >bravel(a)anl.gov -or- > > ravel(a)phys.washington.edu > > Environmental Research Division, Building 203, Room > >E-165 > > Argonne National Laboratory > > phone: (1) 630 252 5033 > > Argonne IL 60439, USA > > fax: (1) 630 252 9793 > > > > My homepage: http://feff.phys.washington.edu/~ravel > > EXAFS software: > >http://feff.phys.washington.edu/~ravel/software/exafs/ > > > > _______________________________________________ > > 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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Re: [Ifeffit] R-factor
by vikrai＠comcast.net 06 Jul '05

06 Jul '05

Alison, I don't think that the difference of R-factors you mention is a big deal. You did not mention in your message more important thing. Did you get the same values of parameters? Besides, it is hardly to expect to find a signal caused by photoelectron backscattering at R<1 A. So the lower limit in R-space fitting equal to 0.1 A is too small probably. As well as the lower limit in q-space fitting because in proteins in this momentum region only full multiple scattering approach should work correct. Victor Krayzman -------------- Original message -------------- > Bruce, > > I've looked, and my R-factors for the back-transformed > space are not necessarily twice the value of the R-factors > for the k-space fits. In fact, they are often quite > close. For example, just recently I had a k-space > R-factor of 0.102 and a q-space R-factor of 0.113. Now, I > realize those numbers are very close, but I'm afraid if I > try to publish this, then I will get criticism for the > q-space R-factors being larger. If I can explain it, then > maybe it won't be a problem. > > I do see what you're saying about the complex vs. real > function, and that definately makes sense, but they don't > differ by a factor of 2. Hmmm. > > alison > > On Wed, 6 Jul 2005 09:43:03 -0500 > Bruce Ravel wrote: > > On Tuesday 05 July 2005 18:39, Alison Costello wrote: > >> I have a question regarding the calculation of the > >>R-factor. I am > >> currently using SIXPACK to process my protein EXAFS > >>data, and I fit the > >> data in both k-space and in q-space (back-transformed > >>k-space). I > >> typically will use k-ranges = [1-13.6] and for > >>multiple-scattering fits, > >> will use an R-range of 0.1 - 4.5. Sometimes, the > >>R-factor for the q-space > >> fit is greater than the R-factor for the k-space fit, > >>which should not be > >> true, as the back-transformed space filters out noise. > >> I am confused as to > >> why this occurs, and am wondering if the R-factor for > >>the back-transformed > >> space is calculated differently than for k-space fits. > > > > Alison, > > > > I would expect the R factor to be bigger in k space due > >to the high frequency > > portions of the data that get filtered out of the q > >space data. That is what > > happened in the one example I just tried. > > > > What are some example values of the R-factors? Do they > >differ by about a > > factor of 2? > > > > One thing that occurs to me is that chi(q) is a complex > >function while chi(k) > > is a real function. In Ifeffit those two functions > >should have the same > > number of points, but the R factor in q is computed > >using both parts of the > > complex function. Thus it would seem reasonable if they > >differed by about 2 > > and there were no significant Fourier components in the > >data beyond your rmax. > > > > B > > > > -- > > Bruce Ravel ----------------------------------- > >bravel(a)anl.gov -or- > > ravel(a)phys.washington.edu > > Environmental Research Division, Building 203, Room > >E-165 > > Argonne National Laboratory > > phone: (1) 630 252 5033 > > Argonne IL 60439, USA > > fax: (1) 630 252 9793 > > > > My homepage: http://feff.phys.washington.edu/~ravel > > EXAFS software: > >http://feff.phys.washington.edu/~ravel/software/exafs/ > > > > _______________________________________________ > > 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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R-factor
by Alison Costello 06 Jul '05

06 Jul '05

I have a question regarding the calculation of the R-factor. I am currently using SIXPACK to process my protein EXAFS data, and I fit the data in both k-space and in q-space (back-transformed k-space). I typically will use k-ranges = [1-13.6] and for multiple-scattering fits, will use an R-range of 0.1 - 4.5. Sometimes, the R-factor for the q-space fit is greater than the R-factor for the k-space fit, which should not be true, as the back-transformed space filters out noise. I am confused as to why this occurs, and am wondering if the R-factor for the back-transformed space is calculated differently than for k-space fits. Thank you. alison

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Too Many Atoms
by rvv052＠mail.usask.ca 01 Jul '05

01 Jul '05

The problem that I have is that with 141 crystallographic sites for a DNA molecule and a space group p 4 2 2, I end up with 611 atoms after running ATOMS. This gives me the error: Feff 6L.02 Fatal Error: Too many atoms in ATOMS list. Maximum is 500. I tries decreasing the number of crystalographic sites by removing hydrogen atoms, but then I got another error: Feff 6L.02 No atoms or overlap cards for unique pot 1 Cannot calculate potentials, etc. Fatal Error: at RDINP. I tried increasing the Rmax as indicated, but this only served to increase the number of atomes, leading me to the error given above. I was hoping that someone could help me with this problem. Remko van den Hurk

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