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ValidatorDB:Database organization

2,315 bytes added, 14:28, 3 September 2014
Details by molecule
==Details by molecule==
[[File:VDB_Residues.PNG|thumb|right|500px650px|The ''synopsis page'Details by molecule''' consists tab contains an interactive table summarizing the results for sets of 6 tabs, two providing support, and four enabling access to molecules sharing the database itselfsame annotation (3-letter code). The support tabs '''Quick Help''' and '''Samples''' help you get started, with basic information and examples Each row recapitulates PDB-wide validation results for each such set of database snippetsmolecules. Various interactive guides are accessible by For a green button at given annotation, 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 Residue''' tab contains an interactive table summarizing the results for each residue validated across sets of molecules sharing the entire PDBsame annotation (3-letter code). Each row corresponds to one residue, identified by its residue name recapitulates PDB-wide validation results for a set of molecules sharing a particular annotation (3-letter code). The information in the table is organized according to the [[ValidatorDB:Analysis_of_Results|validation result]]. The color coding for the table header and the font inside the table is the same , as described in the categories defined in the '''Overview''' tabstep 2. Each element 3 of the table header is described in Data Preparation. For a tool tipgiven annotation, but note that here each column gives the term residue actually refers to occurrence number or percentage of residue (motif)validated molecules which exhibited issues or fared well during a certain validation analysis.
Each row corresponds to one residue, identified by its residue name (3-letter code). The information in the table is organized according to 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''' tab. 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 (motif). 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 graph.
 
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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