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ValidatorDB:Database organization

376 bytes added, 10:31, 5 September 2014
Summary
[[File:VDB_Residue_summary.PNG|thumb|right|650px|The '''Summary''' tab of 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.Note that there the statistics cover only the molecules sharing one annotation (3-letter code)
On If the '''[[ValidatorDB]]''' specifics pageselected molecules more than one annotation (3-letter code) were validated in one run, a list of these residues will be at the first view top of the results is available page. In order to examine the validation summary for each residue, you will need to either click on that specific residue in the '''Summary''' tablist, or just scroll down the page till you reach it. For each Each validated residueis identified by its 3-letter code, as well as its chemical formula and common name. Validation statistics are given as absolute numbers and percentages over all the Summary tab provides an overview of potential issues encounteredmotifs that were processed for each residue.
If more than one residue were validated in one runThe first table with validation results is organized into two main sections, referring to ''incomplete'' (''Missing Atoms'' or ''Rings'') and ''complete structures''. respectively. '''Chirality''' is evaluated only for the complete structures, a list since the absence of these residues will be at some atoms makes it difficult to check the top chirality of some of the pageremaining atoms. In Further, the problematic atoms are highlighted, in order to examine better localize the validation summary for each residue, you will need to either click on that specific residue problems in the list, or just scroll down the page till you reach it. Each validated residue is identified by its 3-letter code, as well as its chemical formula and common name. Validation statistics are given as absolute numbers and percentages over all the motifs that were processed for each residuestructures.
The table Last, a 2D representation of the model residue, and a pie chart with the validation report is organized into two main sectionsresults are provided for visual representation purposes. You can download them via the small icon at the top right corner of the chart, referring to '''incomplete''' (''Missing Atoms'' or ''Rings'') and '''complete structures''' later use them in your presentations. If you click on any validation issue (''With All Atoms'' and ''Rings'') respectivelye.g. The formal distinction between ring atoms and non-ring atoms (simply denoted as atoms) is meant to allow a quick localization of potential issues in residues containing , missing rings, especially where wrong chirality on a specific atom identifiers are not useful. ), you will be redirected to the '''ChiralityDetails''' is evaluated tab where only for the complete structures, since molecules with those specific issues are listed. Results can be interpreted using the absence of some atoms makes it difficult to check information in the chirality of some of the remaining atoms[[ValidatorDB:Database_contents | Database contents]]. Further, the problematic atoms Tool tips are highlighted, in order to better localize available for each element of the problems in the structurestable headers.
Last, a 2D representation The results for different types of the model residue, and a pie chart with the validation results analyses are provided for visual representation purposes. You can download them via labeled using the small icon at the top right corner of the chartunified color scheme: <span style="color:#006400">complete structure and correct chirality</span>, <span style="color:#FF0000">incomplete structure</span>, <span style="color:#DAA520">wrong chirality</span>, and later use them in your presentations<span style="color:#607d8b">warning</span>.
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