NMR Vivaldi

pdbe.org/vivaldi

Vivaldi: Visualisation, analysis and validation of NMR entries
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Welcome to the NMR Vivaldi manual. This manual will provide all essential information for every functionality present in the NMR visualisation tool. The aim of this tool is to interactively explore and validate protein conformations determined by NMR.

This manual is divided in four main sections:



Overview

NMR Vivaldi pages

3D viewer

NMR data

F.A.Q.

Tutorial


NMR Vivaldi pages

Home

Unless one is redirected from the NMR PDBeView pages directly to a visualisation of a specific PDB entry, the NMR Vivaldi home page acts as the front page of the NMR Vivaldi web service. It provides a text-box to gain direct access to the default view of any PDB entry as well as the option to explore different display options of a PDB entry in the NMR Vivaldi wizard.


Wizard

The NMR Vivaldi wizard can be accessed either by clicking the 'Wizard' link located in the service header located at the top-right of NMR Vivaldi interface or through the link on the NMR Vivaldi Home page. It will guide you to select a visualisation type (e.g. domains, RDCs, PROCHECK scores,...) for your preferred PDB entry.

When the wizard page is accessed through the 'Wizard' link or from the NMR Vivaldi Home page while leaving the PDB id search box blank, the first action is to provide the PDB id of interest.

On submitting this PDB id, buttons will appear at the bottom of each visualisation type section Buttons will be greyed and inactive for visualisations that have no data available for the selected PDB id.

All visualisation options are divided in three categories:

Click on the visualisation button of interest to display all possible display styles of the chosen data.

Select the display style of interest and click the 'Display in viewer' button to access the chosen visualisation.

Manual

The NMR Vivaldi manual can be accessed either by clicking the 'Manual' link located in the service header at the top-right of the NMR Vivaldi interface or through the link on the NMR Vivaldi Home page. It is a guide to all functionalities in the NMR Vivaldi service. You are reading it right now!

The manual also includes a frequently asked questions (FAQ) section.

References

  1. W. Rieping, W.F. Vranken (2010) Validation of Archived chemical Shifts through atomic COordinates (VASCO). Proteins 78, 2482-2489.
  2. J.F. Doreleijers*, W.F. Vranken*, C. Schulte*, J. Lin, J. Wedell, C.J. Penkett, G.W. Vuister, G. Vriend, J.L. Markley, E.L. Ulrich (2009) The NMR Restraints Grid (NRG) at BMRB for 5,266 protein and nucleic acid PDB entries. J. Biomol. NMR. 45, 389-396.(* joint first authors)
  3. J.A. Losonczi, M. Andrec, M.W.F. Fischer, J.H. Prestegard (1999) Order Matrix Analysis of Residual Dipolar Couplings Using Singular Value Decomposition. J. Magn. Res. 138, 334-342.
  4. A. Bax, G. Kontaxis, N. Tjandra (2001) Dipolar Couplings in Macromolecular Structure Determination. Methods Enzymol. 339, 127-137.
  5. G. Cornilescu, J.L. Marquardt, M. Ottiger, A. Bax (1998) Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J. Am. Chem. Soc. 120, 6836-6837.

Known issues


3D viewer

The NMR Vivaldi visualisation page for a PDB entry consists of several components which are interactively linked to each other: a title bar containing general info on the PDB id including PDBPrints, an interactive 3D viewer (OpenAstexViewer), a chart/graph, an information section and a tool to save images.

Title bar

The title bar both contains the PDB id and title of the entry currently displayed. It contains quick links to the PDBeView pages for the entry through the PDBPrints widget.

OpenAstex 3D viewer

The OpenAstex 3D viewer offers an interactive view of the selected PDB id and several dropdown menus to change the molecule's appearance in the viewer.

Interacting with the 3D viewer using the dropdown menus:

Direct interactions with the 3D viewer:

Take a look at the information section below: in addition to atom, residue and restraint information, it also contains basic information on the data displayed in the 3D viewer:


Graph

The next section in the NMR Vivaldi interface constitutes a graph capable of displaying several types of experimental NMR data as well as the main navigation through the available NMR data.

Title bar:

Graph:


Information

Next to experimental and validation data shown graphically on the 3D viewer, NMR Vivaldi provides a section containing textual and tabular information interactively when any atom, residue or distance restraint is clicked in the 3D viewer or graph. It also provides basic information on the data displayed in the 3D viewer and on the graph.

Showing and hiding specific types of information: The information section is divided in to several sections, each covering a specific type of information e.g. RDC info, restraint info, etc. As this can become quite a long list of information when each type of data is available for the visualised PDB id, the check boxes provided at the top of this section can be used to toggle the visibility of each type of information.

Types of information:


Saving images

The final section of the NMR Vivaldi interface contains saved images from the graph and OpenAstex 3D viewer. Controls to create snapshots of the graph and 3D viewer are located in the 3D viewer and graph sections of the web page respectively.


NMR data

Scores

Source

Validation residue scores are provided by NRG-CING. Three groups can be distinguished:

Colouring scheme

As a general guide, scores that indicate a good structure are coloured in green, intermediate in orange and bad in red. A continuous colour gradient is applied throughout. Although such colouring scheme is highly informative, it should be treated with care.

CING Red-Orange-Green score

The CING "red-orange-green" score is basically an overall score per residue taking into account all the following WHAT IF and PROCHECK scores as well as constraint violations. Residues are coloured green if all tests are passed, orange if minor issues are observed and red if major issues are observed.

WHAT IF scores

There is a complete description of the output of all WHAT IF checks on the World Wide Web at http://swift.cmbi.ru.nl/gv/pdbreport/checkhelp/.

PROCHECK scores

The G-factor provides a measure of how "normal", or alternatively how "unusual", a given stereochemical property is. In PROCHECK it is computed for the following properties:

The G-factor is essentially a log-odds score based on the observed distributions of these stereochemical parameters.

When applied to a given residue, a low G-factor indicates that the property corresponds to a low-probability conformation. So, for example, residues falling in the disallowed regions of the Ramachandran plot will have a low (or very negative) G-factor. Similarly for unfavourable Chi1-Chi2 and Chi1 values.

Thus, if a protein has many residues with low G-factors it suggests that something may be amiss with its overall geometry.


Chemical Shifts

Source

Validation of chemical shifts is performed by the Validation of Archived chemical Shifts through atomic COordinates (VASCO) service.

This service provides Z-scores for each chemical shift based on two main properties:

Colouring scheme

As a general guide, scores that indicate a good structure are coloured in green, intermediate in orange and bad in red. A continuous colour gradient is applied throughout. Although such colouring scheme is highly informative, it should be treated with care.

Distance Restraints

Source

Experimental distance restraints present at deposition are post-processed at the Biological Magnetic Resonance Bank (BMRB) and added to the NMR Restraint Grid (NRG). The filtered restraints are presented in the NMR Vivaldi viewer.

Types

Experimental distance restraints are grouped in several types:

For each type, one can choose to see all restraints of this type or only violated restraints.

How are violations counted

Every distance restraint has an associated lower and upper limit. Either these values are present within the filtered restraint file generated at BMRB or they are set to be the restraint target value +/- 0.5 Angstrom. If only an upper limit is set, the lower limit is set to 0.0 Angstrom, while when only a lower limit is set, the upper limit is set to 8.0 Angstrom.

Distance restraint violations are calculated per model in an NMR ensemble, so non-integer values might be displayed when a restraint is violated in only a subset of the NMR ensemble.

When a restraint consists of multiple subrestraints (ambiguous restraints), the average distance over all subrestraints is calculated using r-6 weights.

Graph

The distance restraint graph is a per-residue graph and shows the amount of distance restraints or violations per residue. Coloured bars show the averaged values over the whole NMR ensemble, while grey open circles show the individual contributions of the models displayed in the 3D viewer. Additionally, a filled black circle indicates the average over the models displayed in the 3D viewer.

Graphs representing number of restraints are coloured from red (no restraints for the residue) to green (more than 10 restraints per residue).

Graphs representing number of restraint violations are coloured from green (no restraints violated for the residue) to red (more than 1 restraint is violated for this residue).

3D Viewer

Distance restraints or violations can be visualised in the 3D display by clicking on a particular residue in the restraint graph. Only restraints or violations of the type displayed in the graph will be displayed in the 3D viewer.

Restraints within the NMR viewer are coloured by subrestraint. Non-violated subrestraints are displayed as green lines, while violated subrestraints are coloured yellow (violation smaller than 0.3 Angstrom), orange (violation between 0.3 and 0.5 Angstrom) or red (violation greater than 0.5 Angstrom).

Dihedral Restraints

Source

Experimental dihedral angle restraints present at deposition are post-processed at the Biological Magnetic Resonance Bank (BMRB) and added to the NMR Restraint Grid (NRG). The filtered restraints are presented in the NMR Vivaldi viewer.

Types

Experimental are not grouped, but violations can be visualised separately.

How are violations counted

Every dihedral restraint has an associated lower and upper limit. Either these values are present within the filtered restraint file generated at BMRB or they are set to be the restraint target value +/- 20 degrees.

Dihedral restraint violations are calculated per model in an NMR ensemble, so non-integer values might be displayed when a restraint is violated in only a subset of the NMR ensemble.

Graph

The dihedral restraint graph is a per-residue graph and shows the amount of dihedral restraints or violations per residue. Coloured bars show the averaged values over the whole NMR ensemble, while grey open circles show the individual contributions of the models displayed in the 3D viewer. Additionally, a filled black circle indicates the average over the models displayed in the 3D viewer.

Graphs representing number of restraints are coloured from red (no restraints for the residue) to green (more than 1 restraint per residue).

Graphs representing number of restraint violations are coloured from green (no restraints violated for the residue) to red (more than 1 restraint is violated for this residue).

3D Viewer

Dihedral restraints or violations can be visualised in the 3D display by clicking on a particular residue in the restraint graph.

Non-violated restraints and restraints having a violation smaller than 1.0 degree are displayed as green curved lines, while violated restraints are coloured yellow (violation smaller than 3.0 degrees), orange (violation between 3.0 and 5.0 degrees) or red (violation greater than 5.0 degrees).

RDCs

Source

Experimental residual dipolar coupling restraints present at deposition are post-processed at the Biological Magnetic Resonance Bank (BMRB) and added to the NMR Restraint Grid (NRG). The filtered restraints are presented in the NMR Vivaldi viewer.

Post-processing of restraints

Unlike distance restraints or any other type of conventional NMR restraint, the whole set of RDC restraints has to be fitted to an alignment tensor which is generally not deposited by the author. Therefore, NMR Vivaldi performs a basic optimisation protocol based on the Simplex algorithm to calculate the alignment tensor for each member in the NMR ensemble. The method is based on minimising the RMS difference between the experimental and fitted residual dipolar couplings. Tensors are fitted independently for each model.

Residual dipolar couplings are expected to be deposited as reduced values, i.e. converted to the corresponding coupling for a N-H RDC or in their original format. PDBe Vivaldi will try to detect which format is being used and whether the signs of the residual dipolar couplings match. All graphs will present the type of values present in the deposited files.

Graph

Three types of graphs are implemented to visualise RDCs.

3D Viewer

The alignment tensor is represented as a coloured axis frame centred on the molecule. The principal axis (Z) is displayed in red, the second axis (Y) in blue and third axis (X) in yellow.

RDCs are shown as balls and sticks.

Frequently asked questions

Tutorial

A Vivaldi tutorial from 2011 is available here.