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ValidatorDB:Database organization

1,032 bytes added, 11:51, 5 September 2014
Specifics page
==Details==
[[File:VDB_Residue_details.PNG|thumb|right|650px|The '''Details''' tabof the ''specifics page'' serves as a filter based on specific results of the validation analyses, and further enables access to a highly detailed validation report for each validated molecule.]]
Whereas the '''Summary''' tab of the ''synopsis page'' provides statistics, the '''Details''' tab allows you to inspect filter the issues in select groups validation results according to the results of molecules, and further in each individual moleculethe 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 is are organized into a table where each row contains information regarding a single ''validated motifmolecule''. The content Which table columns are filled depends mostly on the state of the filter bar above the table (i.esee description in the next paragraph).The most important columns are ''Id'', ''Issues'', ''Missing atoms/rings'', which motifs are included''Atoms'', and what ''Processing warnings''. The other columns give additional information is displayed) is dictated by , usually helpful in identifying the values source of three selection fields at the top error in the structure. 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 table. Click on molecule's origin, as it contains the first fieldPDB ID, and select as well as the validated residue by its name (3-letter code) from serial index of the drop down menu. Only first atom in the motifs that were matched to that residue name will be displayed ''input motif'', as it appears in the tableoriginal PDB entry. Click on The column ''Issues'' reports the second field and select number of issues found for each particular molecule. The column ''Missing atoms/rings'' explains which atoms are missing in each validated motif, whereas ''Atoms'' shows the type position of issue (e.gincorrect chirality.''Missing atoms'' are listed by their atom identifier in the model, whereas atoms with wrong chirality) from are listed by their identifier in the drop down menuvalidated motif. Only Clicking on a column header allows to sort the motifs which exhibit that type of issue will be displayed according to the property specified in the tableheader. The number of motifs that fit each selection is given Validated molecules where a ''processing warning'' was encountered are marked in brackets. If you want to make your selection even more specific, use the selection filed Id filterorange.
Which As already mentioned, the content of the table columns are filled depends mostly on the type of issue selected in filter bar above the filtertable. The most important columns are validation reports available in the ''Id'Details', ''Issues/Warningstab of the '', ''Missing atoms/rings'', ''Atoms'', ''Processing warningsspecifics page''are organized by annotation (3-letter code). The other columns give additional information, usually helpful in identifying You can easily navigate between reports by selecting the source annotation of interest in the error leftmost drop down menu in the structurefilter bar under the tab names (above the table). The column Id refers Only the table rows with results for the molecules that were matched to a unique identifier assigned that annotation will be displayed. You may further refine the filter according to each individual ''input motif'' the validation issue you are interested in (and thus ''validated molecule'') in order to keep e.g., wrong metal chirality, missing a transparent trace of the molecule's originspecific atom, as it contains the PDB IDcontaining substitutions at a certain position, as well as etc.). Pick the serial index issue of interest from the first atom corresponding drop down menu in the ''input motif'', as it appears 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 original PDB entry. The column ''Issues'' reports filter bar, the number of issues found for each particular moleculemolecules that fit your selection is given in brackets. The column ''Missing atoms/rings'' explains which atoms are missing in each validated motifIf you want to make your selection even more specific, whereas use the ''AtomsId filter'' shows at the position right of incorrect chiralitythe filter bar.  Aside from its filtering function, the '''Missing atomsDetails'' are listed by their atom identifier in the model, whereas atoms with wrong chirality are listed by their identifier in the validated motif' also provides direct access to explicit validation reports for individual molecules. Clicking Just click on a column header allows to sort the motifs according to Id of the property specified molecule of interest in order to be redirected to the headercorresponding validation report.
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