Hi Lisa, Starting from a similar crystal structure could work. Alternatively, building a basic "crystal" structure using symmetry P1 and just putting the atoms where you want them would be feasible - tedious if you have a lot of atoms, easier
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Hi Lisa,

Starting from a similar crystal structure could work.
Alternatively, building a basic "crystal" structure using symmetry P1 and just putting the atoms
where you want them would be feasible - tedious if you have a lot of atoms, easier if you know you
have higher symmetry.

e.g.  Test
Symmetry P1   * i.e. no symmetry
a = 10  b = 10  c = 10   *Angstroms, easy to scale
alpha = 90  beta = 90  gamma = 90  * so metrically cubic

Central atom  0.000  0.000 0.000   * at origin, could always displace by 1/2 lattice constants to keep all in the unit cell
1st NNa    0.220 0.000 0.000   * 1st nns at 2.2 Angstroms away
1stNNb     0.000 0.220 0.000
1stNNc     0.000 0.000 0.220
1stNNd    -0.220 0.000 0.000
etc...

I've used this for modelling molecules, surfaces (with deposited films) as well as 3D crystals.
It is a bit of brute force, but should work in any crystal visualization program...

cheers,
-R.

On 2024-06-27 8:47 a.m., Lisa Langlois wrote:
Hello XAFS friends. I would like to know how to create a structure model for a molecule that was measured with EXAFS, then modeled using the typical strategies? - So, in the end you have some distances and bond angles from the central atom
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Hello XAFS friends.
I would like to know how to create a structure model for a molecule that was measured with EXAFS, then modeled using the typical strategies? - So, in the end you have some distances and bond angles from the central atom to the first, and maybe second neighbor.
I was thinking that you start from a similar crystal structure and then adapt that model using the numbers you got from EXAFS fitting, using for example the Vesta program.
Best wishes,
Lisa.




Lisa Langlois, PhD
Beamline scientist
Rm 144
Phone: +1 225-578-9341
LSU-CAMD
6980 Jefferson Hwy, Baton Rouge, LA 70806
https://www.lsu.edu/camd/