I guess I should elaborate a little -- you can generate a feff.inp file using atoms within artemis and and save the output in another format as well (there are several different options including pdb). The common source would be the atoms.inp file then if you had saved the data beforehand or manually entered information for a new atoms page. If you want to take a feff.inp file and change it to a pdb, you will need to do this yourself. I wrote a perl script to do it (I can see if it is on my laptop tomorrow). I am hardly the Perl master that Bruce is though, perhaps he (or someone else on the list) has written a perl script to make a pdb file from a feff input file (it is just a matter of rearranging and adding additional columns of information). The hardest part, the coordinates are already there. Paul On May 18, 2004, at 10:22 PM, Stefano Ciurli wrote:
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.
I would love to, but I have to head back for some more beam time in Tsukuba as soon as the experiment here ends (I do have Sunday off though (no beam)...
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
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Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons@aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８ 茨城県つくば市東１−１−1 つくば中央第４ 近接場光応用工学センター ポール・フォンス主任研究官