[Ifeffit] graphics and fit

[Stefano Ciurli]

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