This popup allows the user to import, export and view information about individual structures and structure ensembles in the project. Structure ensembles can be split into separate models and individual structures can be merged into ensembles. In addition, RMSDs can be calculated within a superimposed ensemble and displayed on the structure using a colour code and the Structure: Structure Viewer popup.

Viewer

Opens the the Structure: Structure Viewer popup for inspection of the structure.

Ensembles

The {Ensembles} tab lists the current structure ensembles and individual structures in the selected molecular system. Various options are available to edit, import and export structures. Structure ensembles can be split, and individual structure can be merged into ensembles.

The Structure: Structure Ensembles popup (Ensembles).

Molecular System

Specifies the molecular system for which the structure ensembles are listed in the Ensembles table.

Ensembles table

This table contains all the structure ensembles and individual structures in selected molecular system.

#

The ensemble serial number.

Chains

The chains that are present in the structure ensemble.

Residues

The number of residues per structure in the ensemble.

Models

The number of models in the ensemble.

Generation Run

The structure generation run of the ensemble.

Violation Lists

The number of structure violation lists for the ensemble.

Atom Name System

The atom naming system used in the structure ensemble.

Residue Name System

The residue naming system used in the structure ensemble.

Show Coords

Opens the {Coords} tab to display the coordinates of the atoms in the structure ensemble.

Import

Allows the user to import a structure or structure ensemble using the Import PDB file popup.

Export

Allows the user to export a structure or structure ensemble using the Export PDB file popup.

Remove

Removes the selected structures or structure ensembles from the molecular system.

Merge Into Ensemble

Merges a selection of multiple structures into a structure ensemble. The structures have to contain the same atoms.

Split Models

Splits a structure ensemble that consists of multiple models into the individual models.

Align Coords

Aligns the coordinates of the structure ensemble using a best fit routine.

Residues

The {Residues} tab lists the residues in the selected molecular system and some of their structural properties. Various sources of information can be toggled on and off for display in the Residues table.

The Structure: Structure Ensembles popup (Residues).

Ensemble

Specifies the ensemble for which residues and properties are displayed.

CcpCode

Specifies the CcpCode to display parameters only for specific residue types.

Angles

If selected, shows angle information in the Residue table, e.g. phi and psi angles in proteins. In case of a structure ensemble, averages of the ensemble are listed.

RMSDs

If selected, shows the RMSDs in the Residue table, e.g. backbone and all atom RMSDs.

Rama. params

If selected, shows the Ramachandran parameters in the Residue table.

Validation results

If selected, shows a variety of RMSDs calculated for individual atoms in the Residue table.

Residues table

This is the table that lists all the residues and their properties.

Chain

The name of the chain.

Seq Code

The sequence code of the residue.

Ccp Code

The Ccp Code of the residue.

Backbone RMSD

The backbone RMSD value for the residue. This value can be calculated in an ensemble using the [Calculate RMSDs] button.

All atom RMSD

The backbone RMSD value for the residue. This value can be calculated in an ensemble using the [Calculate RMSDs] button.

Φ Angle

The phi angle for a residue in a protein chain.

Ψ Angle

The psi angle for a residue in a protein chain.

Rama. Region

The classification of the residue in the Ramachandran plot region.

Calculate RMSDs

Calculates the RMSDs for the selected ensemble.

View Residue

Labels and focusses on the selected residue in the Structure: Structure Viewer popup.

Display Params

This option applies a colour code and adapts the sizes of atoms for the residues in the Structure: Structure Viewer popup. The colours and sizes of atoms depend on the value of the parameter selected under Validation Parameter (see below). Small atoms and blue colour correspond to small values of the parameter; Large atoms and yellow colours correspond to larger values of the parameter.

Delete Params

Deletes the parameters selected under Validation Parameter (see below).

Validation Parameter

Specifies the parameter that is used for the [Display Params] and [Delete Params] buttons.

Coords

The {Coords} tab lists the atom coordinates for a selected structure model.

The Structure: Structure Ensembles popup (Coords).

Ensemble

Specifies the ensemble from which models are selected for display of coordinates.

Model

Specifies the model in the selected ensemble for which coordinates are displayed.

Coords table

This table lists all the atomic coordinates in the selected model.

#

The atom number.

Atom

The atom name.

Residue

The residue name.

Chain

The chain name.

SeqId

The sequence identifier

x

The x coordinate of the given atom.

y

The y coordinate of the given atom.

z

The z coordinate of the given atom.

Occupancy

The occupancy of the given atom.

B Factor

The B factor of the given atom.

Locn Code

The Locn code of the given atom.