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ValidatorDB:Database organization

1,945 bytes removed, 14:43, 3 September 2014
Details by molecule
[[File:VDB_Residues.PNG|thumb|right|650px|The '''Details by molecule''' tab contains an interactive table summarizing the results for sets of molecules sharing the same annotation (3-letter code). Each row recapitulates PDB-wide validation results for each such set of molecules. For a given annotation, each column gives the number or percentage of validated molecules which exhibited issues or fared well during a certain [[ValidatorDB:Principles#Validation_analyses | validation analysis ]].]]
The '''Details by Residue''' tab contains an interactive table summarizing the results for sets of molecules sharing the same annotation (3-letter code). Each row recapitulates PDB-wide validation results for all molecules sharing a particular annotation (3-letter code). For a given annotation, each column refers to the results from a specific validation analysis. Each cell gives the number (or percentage) of molecules which exhibited issues (missing atoms, wrong chirality, etc.), or fared well (complete structure, correct chirality, etc.) during a given analysis.
The '''Details by Residue''' tab contains an table is interactive table summarizing , allowing efficient sorting and filtering of the results , and direct access to more detailed validation reports for sets the entries of molecules sharing interest. By default, only the same annotation (3-letter code). Each row recapitulates PDB-wide validation results for a set of molecules sharing a particular annotation (3-letter code), as described some analyses are included in step 2the table.3 The complete list of Data Preparationanalyses available in '''ValidatorDB''' is given below the table. For a given annotation, each column gives You may customize the number table by adding or percentage of validated molecules removing columns which exhibited issues or fared well during 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. Regular expressions may be used.
Each row corresponds to one residue, identified by its residue name Click on any molecule annotation (3-letter code). The information in the table is organized according order to access the [['''ValidatorDB:Analysis_of_Results|validation result]]. The color coding for the table header and the font inside the table is the same as in the categories defined in the '''Overview''specifics page'' tab. Each element of with detailed validation results for all molecules in the table header is described in a tool tip, but note PDB which share that here the term residue actually refers to occurrence of residue (motif)particular annotation.
Summary of validation results for sets of molecules sharing the same annotation: This summary is available in tabular form (Supplemental Figure S3). Each row recapitulates PDB-wide validation results for a set of molecules sharing a particular annotation (3-letter code), as described in step 2.3 of Data Preparation. For a given annotation, each column gives the number or percentage of validated molecules which exhibited issues or fared well during a certain validation 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. Clicking on any element in the table header allows to sort the table entries according to that element. Click on any residue name in order to access the '''ValidatorDB''' specifics page with detailed validation results for that residue. The filter at the top right corner allows to retrieve the table row with a specific residue. Simply type the residue name into the filter. All results can be downloaded in *.csv format using the download button at the top left corner. The '''Details by Residue tab''': interactive table summarizing the results for each validated residue across the entire PDB. [[ValidatorDB:Analysis_of_Results |Validation results]] keep the color coding convention, and all results can be downloaded in .csv format. A filter allows to display results only for selected residues. Click on any residue name to access the '''ValidatorDB Specifics page''' with detailed validation results for that residue. Whenever you are unsure about the meaning of individual graphical elements either hover mouse over it or click the green '?' button. The '''Overview''' tab of the ''synopsis page'' provides a very general statistical evaluation of results across the entire PDB in graphical form. The graph summarizes the results for each type of [[ValidatorDB:Principles#Validation_analyses | validation analysis ]], for all validated molecules, irrespective of annotation or PDB entry.  Each colorful bar refers to the number of molecules which exhibited issues (missing atoms, wrong chirality, etc.), or fared well (complete structure, correct chirality, etc.) during a given analysis. The length of the bar correlates with the percentage calculated from the total number of molecules analyzed. A bar appears in the '''Overview''' graph only if it represents at least 0.5%.  Results can be interpreted using the information in the [[ValidatorDB:Database_contents | Database contents]]. Tool tips are available for each element of the graphtable 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>.

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