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ValidatorDB:Database organization

864 bytes added, 14:55, 3 September 2014
Details by PDB entry
==Details by PDB entry==
[[File:VDB_PDBEntries.PNG|thumb|right|500px650px|The ''synopsis page'Details by PDB entry''' consists tab contains an interactive table summarizing the results for sets of 6 tabs, two providing support, and four enabling access to molecules originating from the database itselfsame PDB entry. The support tabs '''Quick Help''' and '''Samples''' help you get started, with basic information and examples of database snippetsEach row recapitulates the validation results for all relevant molecules in a single PDB entry. Various interactive guides are accessible by For a green button at given PDB entry, each column gives the top right corner number or percentage of some tabsvalidated molecules which exhibited issues or fared well during a certain [[ValidatorDB:Principles#Validation_analyses | validation analysis ]].]]
The '''Details by PDB Entry''' tab contains an interactive table summarizing the results for all residues validated in each sets of molecules sharing the same PDB entry. Each row corresponds to one PDB entry, identified by its PDB ID (4-letter code). The information in the table is organized according For a given PDB entry, each column refers to the [[ValidatorDB:Analysis_of_Results|results from a specific validation result]]analysis. The color coding for Each cell gives the table header and the font inside the table is the same as in the categories defined in the '''Overview''' tabnumber (or percentage) of molecules which exhibited issues (missing atoms, wrong chirality, etc. Each element of the table header is described in a tool tip), but note that here the term residue actually refers to occurrence of residue or fared well (motifcomplete structure, correct chirality, etc.)during a given analysis.
The table is interactive, allowing efficient sorting and filtering of the results, and direct access to more detailed validation reports for the entries of interest. By default, only the results of some analyses are included in the table. The complete list of analyses available in '''ValidatorDB''' is given below the table. You may customize the table by adding or removing columns which refer to a certain validation analysis. Clicking on any element in the table header allows to sort the table entries according to that element. The filter at the top right corner allows to retrieve only the results for molecules with certain annotations (3-letter codes), or originating from PDB entries with certain PDB IDs (4-letter codes). Regular expressions may be used. Click on any PDB entry in order to access the '''[[ValidatorDB:Specifics_page| ValidatorDB ''' ''specifics page]]''' with detailed validation results for all residues molecules in that specific PDB entry. Results can be interpreted using the information in the [[ValidatorDB:Database_contents | Database contents]]. Tool tips are available for each element of the table header.  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>.
The filter at the top right corner allows to retrieve the table rows with a specific residue, or the table rows with selected PDB IDs. Simply type the residue name or PDB ID into the filter. All results can be downloaded in .csv format using the download button at the top left corner.
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