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ValidatorDB:Database organization

1,527 bytes added, 07:24, 8 September 2014
Specifics page
Whereas the '''Summary''' tab of the ''synopsis page'' provides statistics, the '''Details''' tab allows you to filter the validation results according to the results of the various validation analyses. Note that you may also access relevant information in the '''Details''' tab by clicking on a specific validation issue in any of the tables in the '''Summary''' tab.
The results acessible by the '''Details''' tab are organized into a table where each row contains information regarding a single ''validated molecule''. Which table columns are filled depends mostly on the state of the filter bar above the table (see description in the next paragraph). The most important columns are ''Id'', ''Issues'', ''Missing atoms/rings'', ''Atoms'', ''Processing warnings''. The other columns give additional information, usually helpful in identifying the source of the error in the structure. The column ''Id'' refers to a unique identifier assigned to each individual ''validated molecule'' in order to keep a straightforward track of the molecule's origin. The ''Id'' contains the PDB ID, as well as the serial index of the first atom in the corresponding ''input motif'' as it appears in the original PDB entry. The column ''Issues'' reports the number of validation issues found for each particular molecule. The column ''Missing atoms/rings'' explains which atoms are missing in each validated molecule, 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 molecule''. Clicking on a column header allows to sort the validated molecules according to the property specified in the header. Validated molecules where a ''processing warning'' was encountered are marked in orange<span style="color:#C68E17">color</span>. For further explanation, please refer to the sections on [[ValidatorDB:Terminology | terminology ]], [[ValidatorDB:Principles | principles ]] and [[ValidatorDB:Database_contents | database contents ]].
As already mentioned, the content of the table depends on the filter bar above the table. The validation reports available in the '''Details''' tab of the ''specifics page'' are organized by annotation (3-letter code). You can easily navigate between reports by selecting the annotation of interest in the leftmost drop down menu in the filter bar under the tab names (above the table). Only the table rows with results for the molecules that were matched to that annotation will be displayed. You may further refine the filter according to the validation issue you are interested in (e.g., wrong metal chirality, missing a specific atom, containing substitutions at a certain position, etc.). Pick the issue of interest from the corresponding drop down menu in the filter bar. Only the table rows with results for the molecules which exhibited that particular issue will be displayed. Whenever you pick something in a drop down menu of the filter bar, the number of molecules that fit your selection is given in brackets. If you want to make your selection even more specific, use the ''Id filter'' at the right of the filter bar.
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==3D visualizationSingle molecule report==[[File:VDB_Details_entry.PNG|thumb|right|650px|'Detailed validation report for a '''single molecule''', accessible by clicking on the respective molecule Id in the '''Details''3D'table of the ''specifics page'' visualization . Consists of a full description for the molecule and detailed the model, complete with references, all resultsfrom all validation analyses, and 3D visualization of all structures involved in the validation process.]]
The 3D viewer implemented in the [[ValidatorDB]] interface '''single molecule report''' offers one step further in a complete image of the analysis of validation results for each individual validated motif, and particular molecule. It is accessible via the '''Details''' tab on the ''specifics page. In the table'', simply click by clicking on the Id (unique identifier containing the PDB ID and a serial number) of a motif the molecule of interest . As you open this report, the molecule Id will appear in order to open the top left corner of the report. The '''single molecule report''' starts with two 3D viewervisualizers, 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 molecule, the input motif , the model, and model residuesuperimpositions of these, in order to help you better assess the position and relevance of the structural issues found during validation(see the full list of terms [[ValidatorDB:Terminology | here]]). AdditionallyAt the top of each visualizer there is a drop down menu where you may choose the structure of interest, along with a few visualization options (atom labels, bonds vs sticks, full screen view). The 2D representation of the model is also provided for clarity, which and is especially helpful for larger motifsmolecules. Basic  Beneath the visualizers, the '''single molecule report''' is organized into three columns, but you may have to scroll down to see all the information about in each column. The left column contains the validated motif is also givenfull identification of the molecule in its original PDB entry, the description of the model and full identification in the wwPDB CCD, along with and a complete report list of [[ValidatorDB:Database_contents#Processing_warnings | processing warnings]], if any were encountered during validation. The middle column lists the validation resultsof the ''completeness'' and ''chirality'' analyses, where all and the right column those of the ''advanced'' analyses (see the potential issues full list of validation analyses [[ValidationDB:Principles#Validation_analyses | here]]). Each problematic atom is listed. The results are listedlabeled 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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[[File:VDB_Warnings.PNG|thumb|right|650px|'''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. Overally a processing warning may simply lead to ignoring a faulty atom, but the motif is validated...include degenerate...
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