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ValidatorDB:Database organization

857 bytes added, 10:12, 5 September 2014
Specifics page
[[File:VDB_Model.png|thumb|right|500px650px|The '''Overview''' tabof the ''specifics page'' provides statistics of the validation results for all selected molecules.]]
To keep consistency with the ''synopsis page'', the '''Overview''' tab on the ''specifics page'' also allows visualization of general validation statistics for the molecules you selected. This representation is entirely compatible with that of the '''Overview''' tab on the ''synopsis page'', and in fact makes up a subset of that data set. The green box above the graph indicates the number of validated molecules, together with their origin.
[[File:VDB_Residue_summary.PNG|thumb|right|500px650px|The '''Summary''' tabof the ''specifics page'' allows easy navigation between annotation-based validation reports. Each report consists of a description of the model corresponding to that annotation, a recapitulation of all validated molecules sharing that annotation, statistics for each validation analysis (completeness, chirality, advanced), and statistics for each problematic atom.]] Next, the corresponding model from wwPDB CCD is briefly described (name, molecular formula, 2D structure, etc.). A recapitulation of all molecules and their respective PDB entries is also included, followed by a table with results of the main validation analyses (completeness, chirality, advanced). For each validation analysis, statistics are provided for all problematic atoms.
On the '''[[ValidatorDB]]''' specifics page, the first view of the results is available in the '''Summary''' tab. For each validated residue, the Summary tab provides an overview of potential issues encountered.
[[File:VDB_Residue_details.PNG|thumb|right|500px650px|'''Details''' tab]]
Whereas the Summary tab provides statistics of the issues over all validated motifs for each validated residue, the '''Details''' tab of the '''[[ValidatorDB]]''' specifics page allows you to inspect the issues in select groups of motifs, and further in each individual motif. Note that you may also access the details of any particular group of motifs also by clicking on a specific issue in any '''Summary''' tab table.
==3D visualization==
[[File:VDB_Details_entry.PNG|thumb|right|500px650px|'''3D''' visualization and detailed results]]
The 3D viewer implemented in the [[ValidatorDB]] interface offers one step further in the analysis of each individual validated motif, and is accessible via the '''Details'' tab on the specifics page. In the table, simply click on the Id of a motif of interest in order to open the 3D viewer, where you can inspect the structural inaccuracies more closely. Here you will be able to view and manipulate with the 3D representations of the validated motif and model residue, to help you better assess the position and relevance of the structural issues found during validation. Additionally, a 2D representation of the model is provided for clarity, which is especially helpful for larger motifs. Basic information about the validated motif is also given, along with a complete report of the validation results, where all the potential issues are listed.
==Processing Warnings==
[[File:VDB_Warnings.PNG|thumb|right|500px650px|'''Processing warnings''' tab]]
The validation reports in ValidatorDB also mention various unusual aspects encountered during validation. Sometimes the processed PDB entries contain information that is ambiguous, conflicting or which deviates strongly from the expected reference. [[ValidatorDB]] reports such events as processing warnings. Such information can be found in the '''Processing Warnings''' tab on the specifics page. The selection field at the top of the page helps filter the warnings for different residues, in case more of them are in validation report. Simply click on the drop down menu and select the category of warnings that you would like to explore. Processing warnings are issues that may cause incorrect Validation, such as bad two residues being too close together (misused concept of alternate conformations) or unusual bond lengths given by the CONECT records. Make sure that negative validation results (e.g., missing atoms) are not in fact caused by ignoring some atoms in an ill-formed structure.

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