What is NCS refinement?

Non-crystallographic symmetry (NCS) can (and in many cases should) be included in refinement. In CNS two models for NCS are available: Strict (constraints) – the model consists of a protomer. Matrices explicitly define the relationship between protomers.

What is crystallography refinement?

X-ray crystal structure refinement, which is the process of achieving agreement between the structural model and the experimental data (structure factors and electron density maps), used to take months and, sometimes, years to complete.

What is rigid body refinement?

Rigid-body refinement is the constrained coordinate refinement of one or more groups of atoms that each move (rotate and translate) as a single body.

What is non crystallographic symmetry?

Noncrystallographic symmetry is present whenever you have collected diffraction data from a crystal containing two or more copies of a molecule where these copies are not related by the normal symmetry of the crystal. The diffraction data provide unique “snapshots” of each copy.

What is R1 and wR2?

wR2 is similar to R1, but refers to squared F-values. This results in wR2 always having a higher value than R1. The final value, GooF, refers to the “goodness of fit” of the solution. In addition to the difference in F values, the GooF also takes into account the number of observed reflections and the parameters used.

How do you cite MolProbity?

Cite MolProbity: Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66:12-21. Davis et al.

What is NCS in Phenix?

Contents. General. Optimization methods. Targets and restraints. Non-crystallographic symmetry (NCS)

What is symmetry crystallography?

symmetry, in crystallography, fundamental property of the orderly arrangements of atoms found in crystalline solids. Each arrangement of atoms has a certain number of elements of symmetry; i.e., changes in the orientation of the arrangement of atoms seem to leave the atoms unmoved.

What is Rwork and Rfree?

Crystallographic Rwork and Rfree values, which are measures of the ability of the models of macromolecular structures to explain the crystallographic data on which they are based, are often used to assess structure quality.

What does MolProbity score mean?

“[The MolProbity score] is a log-weighted combination of the clashscore, percentage Ramachandran not favored and percentage bad side-chain rotamers, giving one number that reflects the crystallographic resolution at which those values would be expected.

What does Clashscore mean?

Noun. clashscore (plural clashscores) (chemistry, of a molecular model) A numerical indication of how many pairs of atoms are unusually close together.

How do you mutate residues in a coot?

If you just want to mutate a particular residue, click on the “go to atom” or F6, then chose your residue. Coot will automatically center its view on the selected residue. Then, click on the “simple mutate” button, click on the residue you want to mutate, and choose by which residue you want to mutate it.

What is coot bond in chemistry?

Coot uses the CSI search from the mmdb library to identify the core fragment of a reference molecule that matches that of a ‘moving’ ligand. Provided that there are more than two such atom pairs, Coot uses the atom-pair list to provide a rigid-body rotation–translation matrix that transforms the ‘moving’ ligand.

How do you open a Phenix?

BECOMING A PHENIX SALON SUITES FRANCHISE OWNER TAKES JUST A FEW SIMPLE STEPS.

1. FRANCHISE COMMITTEE APPROVAL.
2. PRE-QUALIFICATION.
3. FRANCHISE APPLICATION.
4. FRANCHISE DISCLOSURE DOCUMENT (FDD) DELIVERY/BLANK SITE ANALYZER DELIVERY.
5. FRANCHISE OVERVIEW.
6. FINANCING AND FRANCHISEE VALIDATION.
7. VIRTUAL DISCOVERY DAY.

What is glide plane in crystallography?

In geometry and crystallography, a glide plane (or transflection) is a symmetry operation describing how a reflection in a plane, followed by a translation parallel with that plane, may leave the crystal unchanged. Glide planes are noted by a, b or c, depending on which axis the glide is along.

What is glide plane and screw axis?

A screw axis consists of a rotation followed by a translation. Glide plane. A glide plane consists of a reflection followed by a translation. Twofold screw axis applied to a left hand. The hand rotates 180º and moves a half of the lattice translation in the direction of the screw axis, and so on.

What is Chi Square in Rietveld refinement?

The chi2 value is a squared ratio between Rwp and Rexp, i.e. between R-factor from your refinement and R-factor expected from counting statistics.

What is a good Rfree?

Good Values for Free R As a rule of thumb, for models with resolution of 2.0 Å or better (Å values <2.0), free R should not exceed (resolution/10) by more than 0.05; that is, if the resolution is 2.0 Å, free R should not significantly exceed 0.25.

What is a Ramachandran outlier?

Ramachandran outliers are those amino acids with non-favorable dihedral angles, and the Ramachandran plot is a powerful tool for making those evident. Most of the time, Ramachandran outliers are a consequence of mistakes during the data processing.

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