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