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

athena: larger data visualisation window size
by biquard xavier 06 Jul '04

06 Jul '04

Hi ! I have been using athena under LinuX with great satisfaction for a long time now. Recently, I changed my old portable computer for a brand new one: my Xwindow screen size went from 1024x768 to 1920x1250, but all windows opened by athena for data visualisation have the same old size of around 870x670: I cannot take advantage of my new screen size! As I compiled athena from scratch (horae-021), I wonder if I should not modify athena files set_properties.pl and draw_properties.pl that seems to me to be defining window size. If anyone knows for sure how to do it, please let me know! cheers, Xavier -- ------------------------------------------------------------------- Biquard Xavier Tél CEA : 0438785413 CEA-Grenoble Fax : 0438785138 DSM/DRFMC/SP2M/NRS mailto:xbiquard@cea.fr 17, av des Martyrs 38054 Grenoble Cedex 9 ------------------------------------------------------------------- 2nd chance : Tél ESRF1 : 0476882546 Tél ESRF2 : 0476882598 -------------------------------------------------------------------

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updating the faq with OSX-specific information
by Bruce Ravel 05 Jul '04

05 Jul '04

Hi folks, The last email got me thinking about the documentation for the various installers and updaters and such. I would like to ask one of the OSX users on the list to create a new FAQ entry in section 2 explaining how to update Athena and Artemis from source code once Ifeffit has been installed from the OSX disk image. (That is, I'd like an expert OSX user to walk the novice OSX user through the process of building from source and using sudo to install the newly built code.) Similarly, section 2 needs an entry explaining how the unix updater works. I plan to write that in the coming days. A section 2 entry from Carlo or one of the other debian users would probably be a good idea as well. Thanks, 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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ifeffit and Mac OSX
by Matt Newville 04 Jul '04

04 Jul '04

Hi Raja, On Mon, 7 Oct 2002, rajasekaran swaminathan wrote: > Hi Matt, > > I tried again over the past few days to install the binary > installer on my mac (OS X.2). I couldn't find an attached aquaterm > / pgplot demo. The Aquaterm program opens, but I cannot see any > windows come out from that application. I mean, it is just like a > blank application. When I type ifeffit on Terminal app, it doesnt > recognise the presence of ifeffit in the ifeffitosx directory. i.e. > it says that the command is not found. The executable works > perfectly well on a Windows machine, and I was wondering whether > there are any such equivalents for a Macintosh machine. I also dont > think that the installer comes with athena/artemis/tkatoms etc.. Do > you have any other recommendations to resolve this issue? Also,if > it is possible, can I get a CD of these programs for a Macintosh > equivalent to an executable version for the Windows? > > I appreciate your help in this regard. I have used the binary installer once on a OS 10.1 system. It worked for me (after following the simple included instructions, of course) and plotting with Aquaterm did work. I haven't tried 10.2. I know the Mac binary installer does not include athena, artemis, or tkatoms. I believe it only provides the command-line ifeffit. I'm not sure I can answer many other questions about it. I don't know enough about it or 10.2 v. 10.1 issues to know how well it would work with 10.2. If the aquaterm/pgplot demos don't work, I'd guess it's a more serious problem and that the binary installer may not work. Is the Fink / X-Windows / PGPLOT installation procedure too big of a hassle? I know that can work, and that athena will work too. I also believe that the instructions are simpler for 10.2 than 10.1 (especially with respect to getting perl/Tk to work), but haven't tried this myself. I'm copying this message to the ifeffit mailing list, hoping that someone else may have better answers to these questions. How necessary is a complete binary installer for Mac OSX? Thanks, --Matt

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protein data base to feff.inp file
by Kelly, Shelly D. 02 Jul '04

02 Jul '04

Hello All, I just updated my little web page to share the protein data base file converter that I wrote. You can find the perl program and some instructions at: http://www.mesg.anl.gov/exafs.html If you use the program, let me know how it goes. 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 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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