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

Re: [Ifeffit] Atoms restraints
by scalvin＠slc.edu 02 Jul '04

02 Jul '04

If I understand your question correctly, the answer is no. You cannot tell Ifeffit or Artemis to constrain the distance between two atoms with a simple command. The reason is simple--EXAFS doesn't directly contain that information; it only contains it implicitly (maybe). For direct-scattering paths, EXAFS only provides radial information. Multiple-scattering does provide some information along other axes, but this causes a greater effect in some cases than others. What Ifeffit and Artemis do allow is for you to constrain the parameters related to individual scattering paths in pretty much any way you desire. So, for example, you can constrain the distance to the direct scattering path to atom A, the direct scattering path to atom B, and the multiple-scattering path that hits A and B in such a way that the distance between A and B remains constant. But this takes careful geometrical thinking on your part. Incidentally, restraints are different from constraints. "Constraints" are forces and cannot vary. "Restraints" penalize the fit if it drifts too far, but allows some variation. Hope that helps. --Scott Calvin Sarah Lawrence College > So I understand that I can just tell Ifeffit/Artemis: distance between > Atom#1 > and Atom#2 is equal to "x" Angstroms, and that will be forced for all the > next calculations. Did I understand well?? > If this is true I believe that this way is easier than build a lot of > structures to test (If you have more than one histidine the number of > structures increases...). > > Anyway, I had a look at many .inp the examples but I did not understand > well > how to give this command to the program. Can you write me an example? > It would be much easier for me to start from that example and add many > atom-atom distance restraints to keep a rigid structure. > >

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RE: [Ifeffit] Atoms restraints
by Kelly, Shelly D. 02 Jul '04

02 Jul '04

Hi Max, I forgot to include the perl program. Here it is. Shelly > -----Original Message----- > From: Kelly, Shelly D. > Sent: Friday, July 02, 2004 9:55 AM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Atoms restraints > > > Hi Max, > > > > > 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. > > I do not understand this question. What kind of .inp file are you > looking at? Is this the input to feff? The feff.inp file needs to > have a list of atoms with their corrdinates in x, y, and z. > For a hystatine you will want to make a feff.inp file from > the crystal structure. From this list feff makes a theory > that has the contriution to the EXAFS data for each path of > the photo-electron in a different feffxxxx.dat file. Then > Ifeffit/Athena can be used to fit these paths to the data. > During the fitting process you can change the distance > between the atoms by a little bit (<0.5 Angstroms). To > change the distance during the fitting process you need to > define delr for each path included in the fit. > > I am attaching a catalase protien feff.inp file that I made > from a 7CAT.pdb file. > Hum...I see that I wrote a perl program to help do this. I > must appologize that I forgot that I had this program. > Others have asked for it in the past. > > The proceedure that I used to create this file goes like this. > 1) Get your hands on a crystal structure with the same core > hole atom. (i.e. Fe-oxide for my case) > 2) Run atoms inside of Artemis to generate a feff.inp file. > 2b) save the feff.inp file to disk. > 2c) open feff.inp file in a text editor and remove the ipot > and x,y,z coordinates. > 3) Get the pdb file for the protein, or use mine for an > example 7CAT.pdb. > 4) Save the pdf2fi.pl file to disk and the 7CAT.pdb file to disk. > 4b) make the pdf2fi.pl executable by typing "chmod 777 pdf2fi.pl" > 4c) type "pdf2fi.pl 7CAT.pdb" This will generate a > 7CAT.pdb-feff.inp file. This file has the ipot and the x,y,z > coordinates for the atoms in the pdb file. > 4d) To use the program on your own system, open pdf2fi.pl and > edit a few of the lines at the top. Don't worry it is easy > to do and you will not mess it up. You have to tell the > program what atoms are in the pdb file and which one is the core. > 5) paste the file from 4c into the feff.inp file from 2. > 6) Save the feff.inp file to disk and open it in Artemis and run feff. > > > HTH > Shelly >

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RE: [Ifeffit] Atoms restraints
by Kelly, Shelly D. 02 Jul '04

02 Jul '04

Hi Max, > > 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. I do not understand this question. What kind of .inp file are you looking at? Is this the input to feff? The feff.inp file needs to have a list of atoms with their corrdinates in x, y, and z. For a hystatine you will want to make a feff.inp file from the crystal structure. From this list feff makes a theory that has the contriution to the EXAFS data for each path of the photo-electron in a different feffxxxx.dat file. Then Ifeffit/Athena can be used to fit these paths to the data. During the fitting process you can change the distance between the atoms by a little bit (<0.5 Angstroms). To change the distance during the fitting process you need to define delr for each path included in the fit. I am attaching a catalase protien feff.inp file that I made from a 7CAT.pdb file. Hum...I see that I wrote a perl program to help do this. I must appologize that I forgot that I had this program. Others have asked for it in the past. The proceedure that I used to create this file goes like this. 1) Get your hands on a crystal structure with the same core hole atom. (i.e. Fe-oxide for my case) 2) Run atoms inside of Artemis to generate a feff.inp file. 2b) save the feff.inp file to disk. 2c) open feff.inp file in a text editor and remove the ipot and x,y,z coordinates. 3) Get the pdb file for the protein, or use mine for an example 7CAT.pdb. 4) Save the pdf2fi.pl file to disk and the 7CAT.pdb file to disk. 4b) make the pdf2fi.pl executable by typing "chmod 777 pdf2fi.pl" 4c) type "pdf2fi.pl 7CAT.pdb" This will generate a 7CAT.pdb-feff.inp file. This file has the ipot and the x,y,z coordinates for the atoms in the pdb file. 4d) To use the program on your own system, open pdf2fi.pl and edit a few of the lines at the top. Don't worry it is easy to do and you will not mess it up. You have to tell the program what atoms are in the pdb file and which one is the core. 5) paste the file from 4c into the feff.inp file from 2. 6) Save the feff.inp file to disk and open it in Artemis and run feff. HTH Shelly

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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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