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ValidatorDB:Database organization

104 bytes removed, 11:23, 5 September 2014
Details
[[File:VDB_Residue_details.PNG|thumb|right|650px|'''Details''' tab]]
Whereas the Summary tab provides statistics of the issues over all validated motifs for each validated residue, the '''DetailsSummary''' tab of the ''synopsis page'' provides statistics, the ''[[ValidatorDB]]'Details'' specifics page ' tab allows you to inspect the issues in select groups of motifsmolecules, and further in each individual motifmolecule. Note that you may also access relevant information in the details of any particular group of motifs also '''Details''' tab by clicking on a specific validation issue in any of the tables in the '''Summary''' tab table.
The '''Details''' tab is organized into a table where each row contains information regarding a single validated motif. The content of the table (i.e., which motifs are included, and what information is displayed) is dictated by the values of three selection fields at the top of the table. Click on the first field, and select the validated residue by its name (3-letter code) from the drop down menu. Only the motifs that were matched to that residue name will be displayed in the table. Click on the second field and select the type of issue (e.g., wrong chirality) from the drop down menu. Only the motifs which exhibit that type of issue will be displayed in the table. The number of motifs that fit each selection is given in brackets. If you want to make your selection even more specific, use the selection filed Id filter.
Which table columns are filled depend depends mostly on the type of issue selected in the filter. The most important columns are ''Id'', ''Issues/Warnings'', ''Missing atoms/rings'', ''Atoms'', ''Processing warnings''. The other columns give additional information, usually helpful in identifying the source of the error in the structure. Note that complete structures '''do not''' contain columns with the information about missing atoms. The column Id refers to a unique identifier assigned to each individual ''input motif '' (and thus ''validated molecule'') in order to keep a transparent trace of the motifmolecule's origin, as it contains the PDB ID, as well as the serial index of the first atom in the ''input motif'', as it appears in the original PDB entry. The column ''Issues/Warnings'' reports the number of issues or warnings found for each particular motifmolecule. The column ''Missing atoms/rings'' explains which atoms are missing in each validated motif, whereas ''Atoms'' shows the position of incorrect chirality. ''Missing atoms'' are listed by their atom identifier in the model, whereas atoms with wrong chirality are listed by their identifier in the validated motif. Clicking on a column header allows to sort the motifs according to the property specified in the header.
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