Mauro,

With tkatoms you can save your feff.inp in .pdb format and open it with RasMol.

it would be nice to be able, with Tkatoms, to read coordinates from pdb files and output feff.inp files... but maybe this will come. Thank you, Stefano -- ____________________________________________ 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

Hi Bruce,

The notion of having a viewer of ball-and-stick images built into the software is not a new one. Indeed that's part of Cerius and, as I recall, EXAFSPAK does that as well. Maybe others, too. I agree that it's an excellent idea and I certainly understand the value of it. But I don't plan on working on such a tool any time soon.

OK. understandable, but being able to read in Atoms a PDB file would be useful. But see below.

This is correct. Atoms already converts crystallographic data into pdb (and other formats). This can be done with command line atoms, TkAtoms, or Artemis. (And WebAtoms, in principle. It would be easy to do if it doesn't already, which I can't remember one way or the other.) Indeed, any version of atoms can be coerced into writing just about any file for use with a molecule viewer just by creating an appropriate template file.

yes. The problem is to have to input coordinates by hand into Atoms.

Then Stafano wrote:

...

it would be nice to be able, with Tkatoms, to read coordinates from pdb files and output feff.inp files... but maybe this will come.

That question is the exact opposite of your original question. Indeed reading pdb files is one of my eventual goals for Artemis.

I initially was troubled with checking whether I entered the right coordinates (by hand) into the feff.inp file, so that was the reason for my first question (how to draw a pdb file from an .inp file). Then I realized that it would be nice to enter the coordinates into feff.inp from a prepared pdb file, and that was the reason for my second question.

One could jump-start that effort by showing me how it's done, preferably (but not necessarily) in perl.

no idea from me, but others I am sure will help.

In any case, it's not rocket science to make a feff.inp from a PDB.

well, I have been doing it via cut-and-paste, but will look into the following link that you provide.

Look at page 19 of this for an example using a very small PDB: http://cars9.uchicago.edu/xafs/NSLS_EDCA/Sept2002/Ravel.pdf And remember, Feff does NOT require the absorber to be at (0,0,0).

that is a very good hint... I missed it and played around with rotation(translation matrices...) I also posed a question regarding the possibility to treat an imidazole ring as a rigid object, like Excurve is able to do. Any ideas? I am sure someone in the list working on biological samples and using feff has some nice input files for a histidine bound to a metal, with the file usable in a rigid body fit... Stefano -- ____________________________________________ 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

Hello Bruce, I tried to read in a feff.inp file with TkAtoms in order to eventually export it as a pdb file and read it using any molecular viewer. The file is attached and feff6 works well with it. However, when I try to read it in using TkAtoms, I get the following error message: "K": Atoms detected tainted data among the atoms coordinates. The tainted parameter was set to zero then, when I skeptically hit the OK button, I get the subsequent message: Error: unnmatched ) in regex; marked by <-- HERE in m/\bev)<-- HERE \b/ at /Library/Perl/5.8.1/darwin-thread-multi-2level /Xray/Atoms. pm line 462, <$fh> line 2 Any clues to solve this? I suppose it is a matter of feff.inp file format? I am using a free format, and it works for feff6... I am using a G4 Powerbook with OSX 10.3.3 Stefano -- ____________________________________________ 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

Dear Paul, thanks for your message.

As I happen to be in Italy (at Elettra) at the moment and am on the same time, I thought I would reply. Have you tried using the artemis module for reading in the feff.inp file.

yes. I am able to do it and able to run fits with Artemis no problem. I did not realize that Artemis could export feff.inp files to pdb. I tried to: after reading in a feff.inp file, I follow FEFF -> write special output -> pdb, but I get the error message "You did not specify any lattice constant" which of course it is not necessary neither for a feff.inp file nor for a pdb file. So I am stuck.

I have done this many times and successfully exported the pdb file. For viewing the pdb file I used to use vmd (from the University of Illinois -- a free program and capable of ray-tracing and atom selection by type, distance etc.), but now I am using crystalmaker which does more in the crystallography front.

I have VMD installed on my Mac, as well as DeepView, Rasmol, MolMol, iMol, PyMol, O, and Chimera... The problem is not visualizing a PDB file... but rather to export the feff.inp file into a pdb and see what I am actually using, coordinate-wise. Any chance to pass by Bologna for a quick run? I could try to arrange things. Ciao, Stefano -- ____________________________________________ 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"iMol, Dante Alighieri - Inferno - Canto XXVI

On Tuesday 18 May 2004 04:22 pm, Stefano Ciurli wrote:

...

As I happen to be in Italy (at Elettra) at the moment and am on the same time, I thought I would reply.  Have you tried using the artemis module for reading in the feff.inp file.

yes. I am able to do it and able to run fits with Artemis no problem. I did not realize that Artemis could export feff.inp files to pdb. I tried to: after reading in a feff.inp file, I follow FEFF -> write special output -> pdb, but I get the error message "You did not specify any lattice constant" which of course it is not necessary neither for a feff.inp file nor for a pdb file. So I am stuck.

Stefano, You seem to be misunderstanding what functions the various different files play in my software. The purpose of Atoms is to convert crystallographic data into a list of atomic coordinates. Usually this list is in the form of a feff.inp file. Occassionally one might wish to output a file of a different format. In any case a feff.inp file is always the output and never the input. Atoms is built into Artemis and serves the EXACT SAME PURPOSE in that context. I have never written a piece of software that converts a feff.inp file into some other kind of list of atoms nor is it my intention that any of my documentation suggest otherwise. That said, I acknowledge that converting a feff.inp file to a pdb file, although less useful in general than the other way around, would indeed be a nice thing to have. Finally, you underscore another little problem. Atoms (both in the guise of TkAtoms and of Artemis) should fail more gracefully when you choose to import an atoms.inp file and instead select a feff.inp file. I am not sure of a 100% reliable way to handle that problem gracefully, but I will certainly think about it. B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 222 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/