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.
Opens the the Structure: Structure Viewer popup for inspection of the structure.
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).
Specifies the molecular system for which the structure ensembles are listed in the Ensembles table.
This table contains all the structure ensembles and individual structures in selected molecular system.
The ensemble serial number.
The chains that are present in the structure ensemble.
The number of residues per structure in the ensemble.
The number of models in the ensemble.
The structure generation run of the ensemble.
The number of structure violation lists for the ensemble.
The atom naming system used in the structure ensemble.
The residue naming system used in the structure ensemble.
Opens the {Coords} tab to display the coordinates of the atoms in the structure ensemble.
Allows the user to import a structure or structure ensemble using the Import PDB file popup.
Allows the user to export a structure or structure ensemble using the Export PDB file popup.
Removes the selected structures or structure ensembles from the molecular system.
Merges a selection of multiple structures into a structure ensemble. The structures have to contain the same atoms.
Splits a structure ensemble that consists of multiple models into the individual models.
Aligns the coordinates of the structure ensemble using a best fit routine.
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).
Specifies the ensemble for which residues and properties are displayed.
Specifies the CcpCode to display parameters only for specific residue types.
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.
If selected, shows the RMSDs in the Residue table, e.g. backbone and all atom RMSDs.
If selected, shows the Ramachandran parameters in the Residue table.
If selected, shows a variety of RMSDs calculated for individual atoms in the Residue table.
This is the table that lists all the residues and their properties.
The name of the chain.
The sequence code of the residue.
The Ccp Code of the residue.
The backbone RMSD value for the residue. This value can be calculated in an ensemble using the [Calculate RMSDs] button.
The backbone RMSD value for the residue. This value can be calculated in an ensemble using the [Calculate RMSDs] button.
The phi angle for a residue in a protein chain.
The psi angle for a residue in a protein chain.
The classification of the residue in the Ramachandran plot region.
Calculates the RMSDs for the selected ensemble.
Labels and focusses on the selected residue in the Structure: Structure Viewer popup.
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.
Deletes the parameters selected under Validation Parameter (see below).
Specifies the parameter that is used for the [Display Params] and [Delete Params] buttons.
The {Coords} tab lists the atom coordinates for a selected structure model.
The Structure: Structure Ensembles popup (Coords).
Specifies the ensemble from which models are selected for display of coordinates.
Specifies the model in the selected ensemble for which coordinates are displayed.
This table lists all the atomic coordinates in the selected model.
The atom number.
The atom name.
The residue name.
The chain name.
The sequence identifier
The x coordinate of the given atom.
The y coordinate of the given atom.
The z coordinate of the given atom.
The occupancy of the given atom.
The B factor of the given atom.
The Locn code of the given atom.