Main Panel¶
Viewer: Open a graphical display of the current structure
Clone: Clone popup window
Help: Show popup help document
Close: Close popup
Manage Coordinate Structure Ensembles and Models
This system is used to list all of the three-dimensional coordinate information in the CCPN project. This data is organised as structure ensembles that may contain several models, each of which represents a different three-dimensional conformation (albeit only slightly so). All structures in CCPN are describes as ensembles, even if there is only one conformation present. A structure ensemble can be thought of as being equivalent to the ATOM records in a PDB file.
The various tabs list structure ensemble data in tabular form, if a graphical representation of the coordinates is required the user can click on [Viewer] at the upper right of the popup window, after selecting an ensemble in any of the panels.
Ensembles
The first tab contains a table that lists the structure ensembles in the current CCPN project. All structures are associated with a specific molecular system; a group of molecular chains that go together in the same complex or NMR sample. Hence, the “Molecular System” pulldown menu allows the user to switch between structures that correspond to different molecular groupings, although often there will be only one molecular system present.
Structure ensembles may be imported from PDB and PDB-like files via the [Import] function. The associated [Export] will write the selected ensemble to disk in a PDB format; albeit only the ATOM records and using IUPAC atom nomenclature. For a more formal PDB file export the FormatConverter should be used.
The conformational models of a structure ensemble may be split apart into separate entities via [Split Models]; making structures with one model each. Likewise several structure, or ensembles, can be combined into a larger ensemble with [Merge Into Ensemble], assuming that all the structures represent the same set of atoms.
The [Superpose Coords] function will move and rotate the relative relative orientations of the models within an ensemble so that they superpose (spatially align) in an optimal way. This allows for ensemble analyses of structural variation, including the calculation of root mean square deviation (RMSD) values, which gives a measure of coordinate spread. Once the models of an ensemble are superposed the RMSD values will appear in the relevant tables.
Structure Models
The second tab lists all of the conformational models that are present within a structure ensemble (identified by molecular system code and ensemble number) selected in the “Ensemble” pulldown menu. The table lists all of the models with various textual annotations (that can be changes by the user) and RMSD values of each model from the overall ensemble. It should be noted that RMSD values will only be displayed if the models of the ensemble have been superposed, which can be achieved in this tab using [Superpose & Calculate RMSDs].
The lower graph represents the heavy atom backbone and all atom RMSD values for residues across the whole ensemble. Thus the user is able to see any areas of regional variation as far as the molecular sequence is concerned.
Residues
The “Residues” tab lists per-residue information for a structure ensemble selected in the upper left pulldown menu. Additionally the user can choose to display only certain kinds of residue by changing the “Ccp Code” pulldown menu. The main table lists the residues with any RMSD values (if they are calculated during model superposition), backbone dihedral angles and various other structural parameters. Many of the tables columns can be added or removed by checking the various options above the table.
The “Validation Parameter” selection at the bottom right of the panel relates to structure-derived values that may be used to asses the quality of a structure. As standard these will represent various kinds of RMSD value, although other validation parameters may appear from time to time. The chosen set of parameters may be deleted at any time, causing any corresponding column of the table to disappear. The [Display Params] function will use the per-residue values to colour a three-dimensional display of the structure, thus helping to visualise the location of any structural problems.
Coords
The last tab lists all of the coordinate records for a selected conformational model in a selected structure ensemble. These are equivalent to the ATOM records on a MODEL of a PDB file. The table is for display only and cannot currently be edited.
Model Superposition & RMSD Calculation
The way that coordinate superposition is done in Analysis aims to eliminate any need to make any residue or atom selections. The superposition from the inbuilt method should be very good indeed, and aims to give a solution fairly close to global more probabilistic methods. It is however not appropriate for aligning more minor regions of structure that may be connected via a flexible linker to a major globular part; the superposition will converge on the major structured region.
The underlying basis of the method is singular value decomposition to calculate an optimum rotation for two coordinate sets with co-located centroids. Each atom is weighted, both for the SVD and centroid calculation. There are multiple rounds of superimposition to get the ensemble from pairwise model comparison and to better refine the weights.
Initially the weights come from the atomic masses, but in the later stages of the superposition the weights come from the atomic RMSDs calculated in the earlier round. Accordingly, the dissimilar parts have proportionately little influence on the final ensemble (and thus you don’t need to choose the ‘structured’ residues). Precisely, the weights are adjusted to be one over the mean squared deviation (so for an atom RMSD of 0.1 A its weight is 100, but for an RMSD of 3.0 A its weight is 0.111.) and then in the last stage the wighting is exp(-(RMSD/k)^2), which is even more strict (with k=0.8, 0.1 A gives weight=0.98, 3.0 A gives weight=0.00000078),
The superimposition procedure used in Analysis is as follows:
- Translate coordinates to co-locate (weighted) centroids
- SVD superimpose all models to first model; rotation
- Calculate mean and closest model to mean
- Re-calculate weights based upon RMSD
- SVD superimpose again with new weights to closest to mean
- Repeat once again using RMSD-based weights rather than atomic weights
Viewer: Open a graphical display of the current structure
Clone: Clone popup window
Help: Show popup help document
Close: Close popup
A table of the structure ensembles, according to the molecular system they represent
Molecular System: Selects which molecular system (grouping of chains) to show structure ensembles for
Table 1 | |
# | The identification number of the structure ensemble for the molecular system it represents |
Chains | Indicates which chain codes the coordinates of the structure cover |
Residues | The number of residues the coordinates of the structure cover |
Models | The number of conformational models in the structure ensemble |
RMSD | The calculated all-atom root mean square deviation of the whole ensemble, in units of Angstroms |
Generation Run | The name of any structure generation run/job that generated the structure ensemble |
Violation Lists | The number of violation lists that have been calculated for the structure ensemble |
Show Coords: Show a table of atom coordinates for a model from the selected ensemble
Import: Import a structure from file into the CCPN project
Export: Export the selected structure ensemble as a pseudo-PDB format file; no header, ATOM coordinate records only with IUPAC naming
Delete: Delete the selected structure ensemble from the project; any source PDB file remains
Merge Into Ensemble: Merge the selected structures into a single milti-model ensemble; only possible of atom records are identical
Split Models: Split the selected structure ensemble into separate structure records, each containing only one conformational model
Superpose Coords: Perform a two-stage RMSD-weighted superposition of the conformational models in an ensemble; generates RMSD values
A table representing the conformational models in an ensemble and a graph of per-residue RMSDs
Ensemble: Selects which structure ensemble to show the conformational models and RMSD graph for
Superpose & Calculate RMSDs: Calculate all-atom and backbone atom coordinate root mean square deviations for the selected ensemble; fills the graph
Delete Model: Delete the currently selected structural model from the ensemble
Table 2 | |
Model # | The number of the conformational model within the structure ensemble |
Name | A short name for the conformational model, if needed (Editable) |
RMSD | The calculated all-atom root mean square deviation of the model coordinates relative to the whole ensemble |
Details | A user-provided verbose textual comment about the conformational model (Editable) |
A table of residues found in a structure and several per-residue parameters
Ensemble: Selects which structure ensemble to show residue records for
Ccp Code: Allows the residue display to be restricted to only a specific kind of residue, if required
Angles: Whether to show backbone dihedral angles in the table
RMSDs: Whether to show per-residue coordinate RMSD values in the table; calculated within the ensemble
Rama. params: Whether to show the Ramachandran plot regional classification using backbone angles
Validation results: Whether to show per-residue structure validation results (of various types where calculated) in the table
Table 3 | |
Chain | The code of the molecular chain to which the residue belongs |
Seq Code | The sequence number of the residue in its chain |
Ccp Code | The CCPN code for identifying the kind of residue |
Backbone RMSD | The coordinate root mean square deviation for the residue within the ensemble, considering only backbone atoms |
All atom RMSD | The coordinate root mean square deviation for the residue within the ensemble, considering all atoms |
Φ Angle | The phi protein backbone dihedral angle of the residue (C-N-CA-C) |
Ψ Angle | The psi protein backbone dihedral angle of the residue (N-CA-C-N) |
Rama. Region | The region of a Ramachandran plot protein backbone dihedral angles lie in |
Calculate RMSDs: Superpose the conformational models of the selected structure and calculate per-residue and overall RMSD values
View Residue: Open a graphical structure display and label/highlight the selected residue
Display Params: Show the selected set of validation parameters as colors on a graphical structure display
Delete Params: Delete the selected set of structure validation parameters
Validation Parameter: Selects a structure validation parameter to consider; on a graphical structure display of for deletion
A table of the coordinate locations of atoms within a conformational model
Ensemble: Selects which structure ensemble to select a conformational model from
Model: Selects which conformational model within the selected ensemble to display coordinates for
Table 4 | |
# | Number of atom within the structure |
Atom | Name of the atom with coordinates |
Residue | The CCPN code of the residue the atom is in |
Chain | The code of the molecular chain the atom is in |
SeqId | The number of the residue in the sequence; may differ from the molecular system numbering |
x | The atom location along the X-axis, in units of Angstroms |
y | The atom location along the Y-axis, in units of Angstroms |
z | The atom location along the Z-axis, in units of Angstroms |
Occupancy | The fractional occupancy of this coordinate position by the atom |
B Factor | The X-ray crystallographic B-factor |
Locn Code | An alternative location code for coordinate record |
A table and graph of the comparison of structure ensembles
Molecular System: Selects which molecular system (grouping of chains) to compare structure ensembles for
All atoms: Compare all atoms
Backbone only: Compare only backbone atoms
Compare Ensembles: Compare the ensembles; fills the table and graph with RMSD values
Table 5 | |
Ensembles | The ensembles |