Jump to: navigation, search

ValidatorDB:Database organization

234 bytes added, 11:56, 5 September 2014
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 ''input motif'' (and thus ''validated molecule'') in order to keep a transparent trace straightforward track of the molecule's origin, as it . 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 motifmolecule, 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 motifmolecule''. Clicking on a column header allows to sort the motifs validated molecules according to the property specified in the header. Validated molecules where a ''processing warning'' was encountered are marked in orange. 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.

Navigation menu