ABRA: Automated BioEXAFS Refinement & Analysis

Welcome to ABRAs job submission page.

 

Personal Information:

ABRA sends a link of the results automatically to this adress.
E.g. expected results, additional information, feedback, . . .

Your extracted EXAFS data and what you know about it:

Your data file type: Chi(E) (e.g. from KEMP) Chi(k) (e.g. from WinXAS) KEMP/EMBL-type: needs to be in two column format, 1. column containing energy above the edge, 2. column the background-substracted absorption/fluorescence data. Energy must be monotonically increasing. Uploaded filenames should have the suffix .dat.
Upload your data file: WinXAS-type: two column format, 1. column contains k above the edge, 2. column the background-substracted absorption/fluorescence data. k must be monotonically increasing. Uploaded filenames should have the suffix .dat.
Central Atom:
Edge: This corresponds to the element whose absorption edge was used during the EXAFS measurement. Currently only Zn K and Fe K have been fully tested, Mn, Co and Cu are supported, but at your own risk.
Ligands:
Insert the ligands to be included into the modelling of your sample.
(In parenthesis the residue which provides the ligand is given.) Note: For internal reasons the metal contribution is treated as an additional ligand.
Coordinations:
Min Enter minimum coordination of the central atom.
Max Enter maximum coordination of the central atom.
Num Enter the number of central atoms per molecule.
Coordinations for the Ligands defined above will be varied between Min and Max with a stepsize of 1/Num.
Oxidation State: Choose oxidation state. Press CTRL-button and use the mouse to select more the one item. This enables ABRA to use the Bond-Valence-Sum model for scoring. If you do not know the oxidation state of your metal atom select all possible oxidation states for that metal, in this case ABRA will try to determine the oxidation state. Or do not select any oxidation state, the analysis will then run without bond valence sum *not recently tested*.

Experts may change this to fine tune the program - all others should not change anything, keeping the defaults.

DataBase Choose a database of metal-ligand distances to be used in the scoring process. MH+BOK: Radii from Marjorie Hardings WWW target distances (only exception: Fe-His = 2.03) and BVS values from Breese/O'Keefe. MH+BOK_FeS: For Fe-S-clusters, as MH_BOK but with Fe-Fe = 2.72
Restraints: With this option the coordination number of a single ligand can be restrained. E.g. "2,4, 1,8, 1,8" would restrain the coordination of the first ligand to values between 2 and 4, while the second and third ligand may be varried between 1 and 8.
Fit separately:
DW-factor of 1. Ligand
DW-factor of 2. Ligand
DW-factor of 3. Ligand
DW-factor of 4. Ligand
DW-factor of 5. Ligand
Per default the Debye-Waller-factors of all ligands in the first shell are fitted together, which is usually a good assumption. If you have reasons to expect a different vibrational behaviour of a ligand you might consider checking the corresponding box, thereby increasing the number of fit-parameters.
Maximum number of iterations Used during the refinement, usually 200 iterations are more than sufficient.
Fit O/N/Imidazole-radius together: Yes! Per default the radius of oxygen-, nitrogen- and imidazole-ligands are fitted jointly, since their contributions usually can only be distinguished in very good datasets.
Do a restrained refinement afterwards: Yes! Does a restrained refinement, which can help to distinguish His and O ligands.
k-range:

- or -

E-range:

set k-range:

min
max

- or -

set E-range

min
max
The maximum k-range of EXAFS-data is 2-16.5 1/A. You can reduce this values either by a fixed value, or by setting to "Auto", in this case ABRA will try to automatically determine lower/upper limit of the k-range of your data. Alternatively you can specify the energy range, here the maximum k-range is 15.8 to 1078 eV above the edge. Data outside these ranges will be omitted.

EMBL stuff.

Accept our Terms of Usage Yes!

Allow use of your data for further R&D of ABRA. Yes!

This is not mandatory, but highly recommended since it allows us to further improve ABRA.
Reference paper

If this dataset has already been published please enter the corresponding citation here.

           

 

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