Embedded Files
Solving a structure
Solving a structure
Checking the frames and unit cell matching
Checking the frames and unit cell matching
The individual frames are generated into a combined .run file which is then used for the subsequent processing.
[Screenshot - lattice wizard]
Peak hunting works through each frame to check every frame matches the unit cell. Probably not 100% will match, but should be a good result.
Lattice wizard
Data reduction (Peak analysis and identification from XRD frames)
Data reduction (Peak analysis and identification from XRD frames)
The individual frames are then combined into intensities and positions to give an electron density map, but the phase of the wave has not been determined at this stage.
Twinning would be considered at this stage by combining offset data from the twins (two or more crystals).
In most cases, the detected options are usually taken initially, but this step could be revisited later in the process if changes need to be made.
Individual frames could also be removed at this stage, potentially due to bad icing, but usually this would be carried out later, during the structure refinement.
Datasets from multiple crystals of the same compound could also be combined in this stage where necessary.
Data reduction
Crystal face indexing
Crystal face indexing
The software identifies hkl1, and the crystallographer manually assigns the crystal dimensions from the photograph and hkl intersects. This gives the dimensions of the crystal, which is then used in the crystal modelling. This process is repeated for many rotations of the crystal, until the computer is happy that the dimensions have been determined for the crystal.
Data reduction
Data reduction
Numerical absorption for correction of heavy atoms
Numerical absorption for correction of heavy atoms
Text
Space group determination for the unit cell
Space group determination for the unit cell
At this stage a RES file (INS file) is generated which contains all the hkl and structure factor data, with these combined into a single file which can be used to solve an initial model.
Initial solving of the molecular structure
Initial solving of the molecular structure
This step is usually carried out in OLEX2. The solftware uses various models to solve the structure, which includes the phase solving. Generally ShelXT is used initially, but other models can be used if nescessary.
Initial opening of the
ShelXT is selected and a good initial solving of the structure is performed. Note the incorrect atom assignment in the NO2 group where the N is initially shown as a C atom.
Refinement of model
Refinement of model
Crystallographer assigns usnig sense
Atom assignment
Atom assignment
Alteration of atom assignment
Note the incorrect atom assignment in the NO2 group where the N is initially shown as a C atom.
Orbital correction
Orbital correction
Initially each atom is isotropic and is modelled with minimal parameters. The use of orbital correction adds additional parameters which better reflect reality by plotting the atoms aniostropically, which takes into the thermal parameters of each atom.
Note the incorrect atom assignment in the NO2 group where the N is initially shown as a C atom.
Disorder modelling
Disorder modelling
In the model, not every molecule in the crsyal structure sits in exactly the same alignment. This compensates for small amounts of disorder in the individual molecules in the structure, for example rotation of atoms (eg CF3 groups) or disorder in hexyl or isopropyl chains etc
Note the incorrect atom assignment in the NO2 group where the N is initially shown as a C atom.
Modelling of hydrogen atoms
Modelling of hydrogen atoms
At this stage it is usual to assign hydrogen atoms onto the structure, which will see more of the residual electron desity (Q peaks) being replaced by the H atoms.
All non hydrogen atoms have now been modelled. Residual electron density (Q-peaks) can be seen in positions where H atoms are present.
Hydrogen atoms have now been added to the model.
Solvent modelling
Solvent modelling
Where residual density (Q peaks), located far from the structure, the model is refined to try assign the solvent.
Note the incorrect atom assignment in the NO2 group where the N is initially shown as a C atom.
Molecules in the unit cell
Molecules in the unit cell
Could be multiple molecules. These could be mirror images, rotations, improper rotations, glides which are symmetry operations and determined by the space group. These could also be non symmetry operations, where more than one molecule of the compound exists in the unit cell.
Note the incorrect atom assignment in the NO2 group where the N is initially shown as a C atom.
Labelling of the model
Labelling of the model
including unit cell parameters, angles and volume
Assigns atom labels and numbers, and this is refined to make sense. Eg numbering related structures in the same manner.
Note the incorrect atom assignment in the NO2 group where the N is initially shown as a C atom.
cif check the model
cif check the model
Meta data added.
Note the incorrect atom assignment in the NO2 group where the N is initially shown as a C atom.
CIF file is generated
[Example of the text]
CIF check run to validate what's done. Generates a PDF with any issues. [ABCG errors]
Finalising and returning data
Finalising and returning data
Crystallographer checks stuff makes sense. Return to user
Crystal structure database submission
Crystal structure database submission
Crystal structures are routinely deposited into crystal structure databases which allow other researches to access and use the data obtained from single crystal X-ray diffraction.
Information on using CIF files and obtaining information from crystal structures can be found in the X-ray data pages.
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