What is occupancy refinement?


What is occupancy refinement?

Occupancy is related with B-factor. If you try to describe occupancy of ligand from last example as 1.0, B-factor will be too high. In refinement programs occupancy of residues will be refined automatically (if you input more then 1 conformation). It has to be more or less like B-factor of atoms of binding residues.

What is chemical occupancy?

Chemical Occupancy displays the occupancy of any atoms which are not 100% occupied i.e. their occupancy is not 1. As opposed to the “Crystallographic occupancy”, the multiplicity of atoms in special positions will be taken into account.

What is site occupancy factor?

The site occupation factor (sof) gives the probability to find the atom at a specific site. The multiplicity of a site tells the number of atom positions produced by the symmetry of a space group from a single site noted in structure descriptions. CIF, the standard way of telling about a structure, uses sof values.

What does site occupancy mean?

Site Occupancy means a system for monitoring and administering progress of the Work. Site occupancy involves the Contract Administrator setting a completion date for the Work along with a daily Contract Administration cost (Site Occupancy cost) for each Working Day the contractor is able to work.

What is atomic occupancy?

When researchers build the atomic model of these portions, they can use the occupancy to estimate the amount of each conformation that is observed in the crystal. For most atoms, the occupancy is given a value of 1, indicating that the atom is found in all of the molecules in the same place in the crystal.

What is site occupancy?

How does Rietveld refinement work?

Rietveld refinement is a technique described by Hugo Rietveld for use in the characterisation of crystalline materials. The neutron and X-ray diffraction of powder samples results in a pattern characterised by reflections (peaks in intensity) at certain positions.

What is Biso factor?

Negative value of Biso means that there are some other factors influencing intensities – preferred orientation/disorder at different sites, which are not taken into account in your current model. Strongly negative values of Biso, less than -0.3 means that something is really wrong.

What is the measurement of site occupancy?

The site occupancy index indicates how many square metres of surface area can be built per square metre of land. An area of land measuring 1,000 m² with a site occupancy index of 0.7 means that 700 m² in total can be built on it.

What is occupancy crystallography?

”The occupancy nj of atom j is a measure of the fraction of molecules in the crystal in which atom j actually occupies the position specified in the model. If all molecules in the crystal are precisely identical, then occupancies for all atoms are 1.00.

What is a site occupancy model?

The basis of occupancy model is that there are two stochastic processes occurring that affect whether a species is detected at a site. A site may be either occupied or unoccupied by the species; if it is occupied then at each visit there is some probability of detecting the species.