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ValidatorDB:Database organization

251 bytes removed, 11:13, 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 validation reports available in the corresponding model from wwPDB CCD is briefly described '''Summary''' tab of the ''specifics page'' are organized by annotation (name, molecular formula, 2D structure, etc.3-letter code). A recapitulation of all molecules and their respective PDB entries is also included, followed You can easily navigate between reports by a table with results clicking on the annotation of interest in the main validation analyses (completeness, chirality, advanced)bar under the tab names. For each validation analysis, statistics are provided for all problematic atoms. Note that there the statistics cover only Each report consists of information about the model and validated molecules sharing one corresponding to that particular annotation (3-letter code).

If First, the selected model from wwPDB CCD is briefly described by name, molecular formula, 2D structure, etc. Next, a recapitulation of all molecules more than one annotation (3-letter code) were validated in one runand their respective PDB entries is also included, followed by a list table with results of these residues will be at the top of the pagemain validation analyses (completeness, chirality, advanced). In order to examine the For each validation summary analysis, statistics are provided for each residue, you will need to either click on all problematic atoms. Note that specific residue in here the list, or just scroll down statistics cover only the page till you reach it. Each validated residue is identified by its molecules sharing this annotation (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 residue).

The first table with validation results is organized into two main sections, referring to ''incomplete'' (''Missing Atoms'' or ''Rings'') and ''complete structures''. respectively. The section with ''complete structures'Chirality'is further organized into subsections based on the results of the '' chirality'' and ''advanced'' analyses. Specifically, a general distinction is evaluated only for the made between ''complete structures, since the absence of some atoms makes it difficult to check the '' with ''correct chirality'' and with ''wrong chirality of some of the remaining atoms''. Further, the problematic atoms Warnings like ''foreign atom'' and ''substitutions'' are highlighted, in order to better localize the problems in the structuresalso included.

Last, a 2D representation of the model residue, Subsequent tables highlight and a pie chart with the validation results are provided provide statistics for visual representation purposes. You can download them via the small icon at problematic atoms, in order to better localize the top right corner of problems in the chart, and later use them in your presentationsstructures.

If you click on any validation issue (e.g., missing rings, wrong chirality on a specific atom), you will be redirected to the '''Details''' tab where only the molecules with those specific issues are listed. Results can be interpreted using the information in the [[ValidatorDB:Database_contents | Database contents]]. Tool tips are available for each element of the table headers.

Results can be interpreted using the information in the [[ValidatorDB:Database_contents | Database contents]]. Tool tips are available for each element of the table headers. The results for different types of validation analyses are labeled using the unified 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>, <span style="color:#607d8b">warning</span>.

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