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ValidatorDB:Database organization

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Synopsis page
In '''ValidatorDB''', the results of the validation analyses are organized systematically, ranging from detailed reports for single molecules, to a PDB-wide general summary, and fully customized reports. To facilitate interpretation, access is provided in graphical and tabular form via different sections of the web interface.
'''ValidatorDB''' is organized on two main levels, namely PDB-wide validation statistics (synopsis page), and detailed validation reports for specific molecules of interest (specifics page). We shall describe each level of the database in detail below. The database or various sections of it can be downloaded in .csv or .JSON format, along with the 3D structure files of all models, input motifs and validated molecules.
===Synopsis page=== [[File:VDB_intro.png|thumb|right|500px|The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. The support tabs '''Quick Help''' and '''Samples''' help you get started, with basic information and examples of database snippets. Various interactive guides are accessible by a green button at the top right corner of some tabs.]]
The '''ValidatorDB''' synopsis page contains a brief description of '''ValidatorDB''', along with information about the last database update (date and number of structures that have been processed during the validation). Specifically, in May 2014, over 100,000 PDB entries had been processed, containing over 230,000 molecules relevant for validation, and approximately 17,000 different models were used as reference during validation.
The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. Since this is your first contact with the database, the support tabs '''Quick Help''' and '''Samples''' help you get started, with basic information and examples of database snippets. Various interactive guides are accessible by a green button at the top right corner of some tabs. Examples of more complex analyses are available as ''[[ValidatorDB:CaseStudies | case studies]]''.
The '''ValidatorDB''' synopsis page further provides access to various data sets of PDB-wide validations via four different tabs, namely '''Overview''', '''Details by Residue''', '''Details by PDB entry''' and '''Custom Search'''. A full description of each of these tab is given below. {| class="wikitable" border="1" style="margin: 1em auto 1em auto;" width="650px"
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|<!--Col1-->1 The '''Synopsis synopsis page''' contains a general description, and is organized in consists of 6 tabs, namely two providing support, and four enabling access to the database itself. The support tab '''Quick Help'', ''Samples''helps you get started, ''Overview'', ''Details by Residue'', ''Details by PDB Entry'' and ''Custom Search''. These tabs provide access with basic information about how to graphical and tabular overviews and statistical evaluation of validation results for get oriented in the entire PDB, for each residue across all PDB IDs containing that residue, and for all analyzed residues in each PDB ID, respectivelyweb page. Click on each tab to discover what type Various interactive guides are accessible by a green button at the top right corner of overview can be accessedsome tabs. Whenever you Tool tips are unsure about available for most of the meaning of individual graphical elements either hover mouse over it or click the green '? Guide' button. |<!--Col2-->2. The '''Samples page''' contains several tab offers basic examples of database snippets, along with a short description brief interpretation of results. Two categories of sample validation reports (Molecules, PDB Entry) illustrate interesting cases of molecules with a high or low number of errors. Additionally, the Step-by-Step category contains video tutorials and slides explaining how to obtain such results . Examples of both validated residues and PDB entriesmore complex analyses are available as ''[[ValidatorDB:CaseStudies | case studies]]''.
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AdditionallyThe '''ValidatorDB''' synopsis page further provides access to various data sets. You may retrieve specific validation reports using the '''[[ValidatorDB:Database_organization#Search | Search]]''' tab. Further, the results from PDB-wide validations are available via three different tabs, namely '''[[ValidatorDB:Database_organization#Overview | Overview]]''', '''[[ValidatorDB:Database_organization#Details_by_molecule | Details by molecule]]''' and '''[[ValidatorDB:Database_organization#Details_by_PDB_entry | Details by PDB entry]]''synopsis page'. A full description of each of these tab is given in their respective sections.  ==Search== [[File:ValidatorDB-Search By Entry and Annotation.png|thumb|right|650px|The '''Search tab''' allows to access retrieve validation reports for specific molecules. You may use several search criteria, namely by PDB entry (4-letter code), by molecule identifier (PDB ID: residue ID chain), molecule annotation (3-letter code), or a combination of the PDB entry and molecule annotation (shown here). In each case you will be provided with an input field, where you can enter a list of values for the relevant criterion. Examples and tool tips are provided for easy reference with respect to the expected syntax.]] '''ValidatorDB''' contains validation results for the entire Protein Data Bank. You are probably interested only in a subset of these (e.g., the validation results for a specific residues of interest inhibitor which appears in the PDB entry you plan to use further in your simulations). The ''synopsis page'' allows to access specific validation reports via the '''Quick Lookup barSearch tab''' at .  You may define the search using several criteria, namely PDB entry (4-letter code), molecule identifier (PDB ID: residue ID chain), molecule annotation (3-letter code), or a combination of the bottom PDB entry and molecule annotation. The syntax of the pagesearch is quite simple, but you can always check out the examples and tool tips if you want to make sure. Click on criterion you plan to use. Simply type In each case, there will be an input field where you can enter a comma or new line separated list of residue values for the relevant criterion. You may prefer to use the advanced search functions available on the Protein Data Bank web page, in order to generate a list of relevant annotations (3-letter codes) into and PDB IDs. Instructions on how to achieve this are included in the web page as a tool tip.  Once you click the blue search button at the bottom of the page, the validation results for the molecules you specified according to the chosen criteria are then retrieved from '''Quick Lookup barValidatorDB''', organized and made accessible via a unique ''[[ValidatorDB:Database_organization#Specifics_page | specifics page]]'', which you will be redirected to the can access at a later time via its unique URL. The ''[[ValidatorDB:Database_organization#Specifics_page | specifics page]] containing '' is described in detail in the second part of the ''Data organization'' section of this manual. The last 10 searches you performed are listed for your convenience.  <br style="clear:both" /> ==Overview==[[File:VDB_overview.png|thumb|right|650px|The '''Overview tab''' contains an overall validation results report for all the ligands and non-standard residues in the Protein Data Bank. Each bar represents overall statistics for the molecules you requested[[ValidatorDB:Database_contents | results ]] of a certain type of [[ValidatorDB:Principles#Validation_analyses | validation analysis ]]. If you specify ]] The '''Overview''' tab of the ''synopsis page'' provides a list very general statistical evaluation of results across the entire PDB IDs (4-letter codes) instead, then in graphical form. The graph summarizes the corresponding results for each type of [[ValidatorDB:Database_organizationPrinciples#Specifics_page Validation_analyses | specifics pagevalidation analysis ]] will contain validation results , for all relevant validated molecules in the , irrespective of annotation or PDB entries you specifiedentry.
====Overview====[[File:VDB_overviewEach 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.png|thumb|right|500px|The ''synopsis page'' consists length of 6 tabs, two providing support, and four enabling access to the database itselfbar correlates with the percentage calculated from the total number of molecules analyzed. The support tabs A bar appears in the '''Quick HelpOverview''' and '''Samples''' help you get started, with basic information and examples of database snippetsgraph only if it represents at least 0. Various interactive guides are accessible by a green button at the top right corner of some tabs5%.]]
The Overview tab of Results can be interpreted using the synopsis page provides a very general statistical evaluation of results across information in the entire PDB in graphical form[[ValidatorDB:Database_contents | Database contents]]. The elements of the graph represent percentages of the total number of motifs (over 200,000) of residues relevant Tool tips are available for validation. A graphic element will be displayed in the '''Overview''' graph only if it represents at least 0.5% of the total number of motifs. Each each element of the graph is described in a tool tip, but note that here the term residue actually refers to occurrence of residue (motif).
The elements results for different types of validation analyses are labeled using the graph can be assigned to roughly 6 categories, depending on which kind of information they contain (e.g.unified color scheme: <span style="color:#006400">complete structure and correct chirality</span>, <span style="color:#FF0000">incomplete residuestructure</span>, <span style="color:#DAA520">wrong chirality issues, warnings</span>, etc). The categories are marked by different colors. All the graph elements are explained in the [[ValidatorDB<span style="color:Analysis_of_Results| results section]]#607d8b">warning</span>.
Note that this table can be downloaded in a *.csv format after clicking 'CSV' in the bottom right corner of the infographics.
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[[File:VDB_Residues.PNG|thumb|right|500px|The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. The support tabs '''Quick Help''' and '''Samples''' help you get started, with basic information and examples of database snippets. Various interactive guides are accessible ==Details by a green button at the top right corner of some tabs.]]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 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 all molecules sharing a particular annotation (3-letter code). The information in the table is organized according For a given annotation, 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. Click on any residue name in order The filter at the top right corner allows to access retrieve only the '''ValidatorDB''' specifics page with detailed validation results for that residuemolecules with certain annotations. Regular expressions may be used.
The filter at the top right corner allows Click on any molecule annotation (3-letter code) in order to retrieve access the table row '''ValidatorDB''' ''specifics page'' with a specific residue. Simply type the residue name into the filter. All detailed validation results can be downloaded for all molecules in *.csv format using the download button at the top left cornerPDB which share that particular annotation.
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=Details by PDB entry==="color:#607d8b">warning</span>.<br style="clear:both" />
[[File:VDB_PDBEntries.PNG|thumb|right|500px|The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. The support tabs '''Quick Help''' and '''Samples''' help you get started, with basic information and examples of database snippets. Various interactive guides are accessible ==Details by a green button at the top right corner of some tabs.]]PDB entry==
[[File:VDB_PDBEntries.PNG|thumb|right|650px|The '''Details by PDB Entryentry''' tab contains an interactive table summarizing the results for sets of molecules originating from the same PDB entry. Each row recapitulates the validation results for all residues validated relevant molecules in each a single PDB entry. Each row corresponds to one For a given PDB entry, identified by its PDB ID (4-letter code). The information in the table is organized according to each column gives the number or percentage of validated molecules which exhibited issues or fared well during a certain [[ValidatorDB:Analysis_of_ResultsPrinciples#Validation_analyses |validation resultanalysis ]]. 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).]]
The table is interactive. Clicking on any element in the table header allows to sort the table entries according to that element. Click on any PDB in order to access the '''[[ValidatorDB:Specifics_page| ValidatorDB specifics page]]Details by PDB Entry''' with detailed validation tab contains an interactive table summarizing the results for all residues in that sets of molecules sharing the same PDB entry. Each row corresponds to one PDB entry, identified by its PDB ID (4-letter code). For a given PDB entry, 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 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 table rows results for molecules with a specific residuecertain annotations (3-letter codes), or the table rows originating from PDB entries with selected certain PDB IDs(4-letter codes). Simply type the residue name or PDB ID into the filter. All results can Regular expressions may be downloaded in .csv format using the download button at the top left cornerused.
Click on any PDB entry in order to access the '''ValidatorDB''' ''specifics page'' with detailed validation results for all molecules in that specific PDB entry.
====Custom Search====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.
[[File:VDB_Custom.PNG|thumb|right|500px|The ''synopsis page'' consists results for different types of 6 tabsvalidation analyses are labeled using the unified color scheme: <span style="color:#006400">complete structure and correct chirality</span>, two providing support<span style="color:#FF0000">incomplete structure</span>, and four enabling access to the database itself. The support tabs '''Quick Help''' and '''Samples''' help you get started<span style="color:#DAA520">wrong chirality</span>, with basic information and examples of database snippets. Various interactive guides are accessible by a green button at the top right corner of some tabs<span style="color:#607d8b">warning</span>.]]
The '''Custom Search''' tab allows you to create your own view of the ligands validation of the PDB database. Simply paste a list of your desired ligands (3-letter code) and/or PDB entries (4-letter code) in provided text boxes separated by commas or a newlines. This is particularly convenient in case you need to retrieve a validation report for a huge number of structures. Such as all the ''glycosyltransferases'' or ''nmr structures''. Note that you can retrieve such lists by using [http<br style="clear:both" //www.rcsb.org/pdb/search/advSearch.do advanced search in PDB]. Also bear in mind that each of these custom searches will be assigned a unique permanent web address, so you can access these results later on. Also a list of your last custom searches is provided for your convenient.>
=Specifics page=
For the description of all the elements of Specifics page, please follow this The '''[[ValidatorDB:Specifics page|link]]''' ''specifics page'' provides detailed validation reports for various selections of the database. Such reports include a validation summary and detailed information in both tabular and graphical form, along with a 3D structure visualizer for closer inspection of the problematic structures.
The ''specifics page'' is accessible from the ''[[ValidatorDB:Database_organization#Synopsis_page | synopsis page]]'', either via the '''Quick Lookup''' bar, or via any single entry in the tables from the '''Details by molecule''' and '''Details by PDB entry'''. Depending on how it was accessed, the '''specifics page''' might retrieve validation results for one or more molecules, a fact mentioned at the very top of the page.
The validation results are accessible in tabular and graphical form via several tabs on the '''[[ValidatorDB]] specifics page''' is accessible from the [[ValidatorDB#Synopsis_page | synopsis page]], either via the namely '''LookUp barOverview''' on the , '''OverviewSummary''' tab, or via the residue names and PDB IDs in the interactive tables on the tabs '''Details by Residue''' and '''Details by PDB EntryProcessing Warnings''', respectively. Depending on how it was accessed, These are described in detail in their respective sections below. It is important to note that the '''specifics page''' might retrieve contains annotation-based validation reports. This means that if the molecules you selected share the same annotation (3-letter code), all results will be included in a single report. However, you may have retrieved validation results for molecules with different annotations, as is the case with PDB entries containing many different ligands for instance. In this case, the validation results will be organized according to annotation. Specifically, there will be as many reports as there are annotations. All tabs on the ''specifics page'' discuss one or more residuesreport at a time, a fact mentioned at and allow easy navigation between these reports. The only exception is the very top of '''Overview''' tab, which presents the pagetotal statistics for all validated molecules, and not per annotation.
The '''[[ValidatorDB]]''' specifics page provides a straightforward report of the validation results, including a summary and detailed information in both tabular and graphical form, along with a 3D structure visualizer for closer inspection of the problematic structures. These reports are accessible via several tabs on the specifics page, namely '''Overview''', '''Summary''', '''Details''' and '''Processing Warnings'''. These are described in detail in the section below. Inspecting the tabular and graphical validation reports accessible on the specifics page is the most comfortable and effective way to evaluate the results. Additionally, you You may use the JSON Data download button at the top right corner of the specifics page in order to download the complete validation reports and perform any additional analyses on your own.
==Overview==
[[File:VDB_Model.png|thumb|right|500px650px|The '''Overview''' tabof the ''specifics page'' provides statistics of the validation results for all selected molecules.]]
To keep consistency with the ''synopsis page'', the '''Overview''' tab on the ''specifics page '' also allows visualization of general validation statistics for a the molecules you selected number of residues via the Overview tab. This representation is entirely compatible with that of the '''Overview''' tab on the ''synopsis page'', and in fact makes up a subset of that data set. All color coding conventions are keptThe green box above the graph indicates the number of validated molecules, and tool tips provide descriptions of each graphical elementtogether with their origin.
Note that this statistics can be downloaded in a *.csv format after clicking 'CSV' in the bottom right corner All color coding conventions are kept (<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>), and tool tips provide descriptions of the infographicseach graphical element.
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==Summary==
The validation reports available in the '''Summary''' tab of the ''specifics page'' are organized by annotation (3-letter code). You can easily navigate between reports by clicking on the annotation of interest in the bar under the tab names. Each report consists of information about the model and validated molecules corresponding to that particular annotation. {| class="wikitable" border="1" style="margin: 1em auto 1em auto;" |- |<!--Col1-->[[File:VDB_Residue_summary.PNG|thumb650px]] |right<!--Col2-->[[File:VDB_Entry_summary.PNG| 650px]] |500px- |<!--Col1-->The '''Summary''' tab]]of the ''specifics page'' for all molecules sharing a '''specific annotation (3-letter code)'''. The<br/> report consists of a description of the model corresponding to that annotation, a recapitulation of all validated<br/> molecules sharing that annotation, statistics for each validation analysis (completeness, chirality, advanced),<br/> and statistics for each problematic atom. |<!--Col2--> The '''Summary''' tab of the ''specifics page'' for a '''single PDB entry''' allows easy navigation between annotation-based<br/> validation reports. Each report consists of a description of the model corresponding to that annotation,<br/> a recapitulation of all validated molecules sharing that annotation, statistics for each validation analysis<br/> (completeness, chirality, advanced), and statistics for each problematic atom. |}
On First, the '''[[ValidatorDB]]''' specifics pagemodel from wwPDB CCD is briefly described by name, the first view molecular formula, 2D structure, etc. Next, a recapitulation of the all molecules and their respective PDB entries is also included, followed by a table with results is available in of the '''Summary''' tabmain validation analyses (completeness, chirality, advanced). For each validated residuevalidation analysis, statistics are provided for all problematic atoms. Note that here the statistics cover only the Summary tab provides an overview of potential issues encounteredmolecules sharing this annotation (3-letter code).
If more than one residue were validated in one run, a list of these residues will be at the top of the page. In order to examine the The first table with validation summary for each residueresults is organized into two main sections, you will need referring to either click ''incomplete'' (''Missing Atoms'' or ''Rings'') and ''complete structures''. respectively. The section with ''complete structures'' is further organized into subsections based on that specific residue in the list, or just scroll down results of the page till you reach it''chirality'' and ''advanced'' analyses. Each validated residue Specifically, a general distinction is identified by its 3-letter code, as well as its chemical formula made between ''complete structures'' with ''correct chirality'' and common namewith ''wrong chirality''. Validation statistics Warnings like ''foreign atom'' and ''substitutions'' are given as absolute numbers and percentages over all the motifs that were processed for each residuealso included.
The table with the validation report is organized into two main sections, referring to '''incomplete''' (''Missing Atoms'' or ''Rings'') and '''complete structures''' (''With All Atoms'' and ''Rings'') respectively. The formal distinction between ring Subsequent tables highlight problematic atoms and non-ring atoms (simply denoted as atoms) is meant to allow a quick localization of potential issues in residues containing rings, especially where atom identifiers are not provide useful. '''Chirality''' is evaluated only for the complete structures, since the absence of some atoms makes it difficult to check the chirality of some of the remaining atoms. Further, the problematic atoms are highlightedstatistics, in order to better localize the problems in the structures.
LastIf you click on any validation issue (e.g., missing rings, wrong chirality on a 2D representation of specific atom), you will be redirected to the '''Details''' tab where only the model residue, and a pie chart molecules with the validation results those specific issues are provided for visual representation purposeslisted. You  Results can download them via be interpreted using the information in the small icon at [[ValidatorDB:Database_contents | Database contents]]. Tool tips are available for each element of the top right corner table headers. The results for different types of validation analyses are labeled using the chartunified color scheme: <span style="color:#006400">complete structure and correct chirality</span>, and later use them in your presentations<span style="color:#FF0000">incomplete structure</span>, <span style="color:#DAA520">wrong chirality</span>, <span style="color:#607d8b">warning</span>.
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==Details==
[[File:VDB_Residue_details.PNG|thumb|right|650px|The '''Details''' tab of 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==[[File:VDB_Residue_details''' tab allows you to filter the validation results according to the results of the various validation analyses.PNG|thumb|right|500px|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.
Whereas The results acessible by the Summary '''Details''' tab provides statistics 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 issues over all validated motifs for each validated residuefilter bar above the table (see description in the next paragraph). The most important columns are ''Id'', ''Issues'', ''Missing atoms/rings'', the ''Atoms'', 'Details'Processing warnings'' tab . The other columns give additional information, usually helpful in identifying the source of the error in the structure. The column ''Id''[[ValidatorDB]]refers to a unique identifier assigned to each individual ''validated molecule'' specifics page allows you in order to inspect keep a straightforward track of the molecule's origin. The ''Id'' contains the issues in select groups PDB ID, as well as the serial index of motifs, and further the first atom in each individual the corresponding ''input motif'' as it appears in the original PDB entry. Note that you may also access The column ''Issues'' reports the details number of any validation issues found for each particular group molecule. The column ''Missing atoms/rings'' explains which atoms are missing in each validated molecule, whereas ''Atoms'' shows the position of motifs also incorrect chirality. ''Missing atoms'' are listed by clicking their atom identifier in the ''model'', whereas atoms with wrong chirality are listed by their identifier in the ''validated molecule''. Clicking on a specific issue column header allows to sort the validated molecules according to the property specified in any the header. Validated molecules where a ''processing warning'Summary''' tab tablewas encountered are marked in <span style="color:#C68E17">color</span>. 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 is organized into a table where each row contains information regarding a single validated motif. The content of the table (i.e., which motifs ''specifics page'' are included, and what information is displayed) is dictated by the values of three selection fields at the top of the table. Click on the first field, and select the validated residue organized by its name annotation (3-letter code) from . You can easily navigate between reports by selecting the annotation of interest in the leftmost drop down menuin the filter bar under the tab names (above the table). Only the motifs table rows with results for the molecules that were matched to that residue name annotation will be displayed in the table. Click on You may further refine the second field and select filter according to the type of 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 menuin the filter bar. Only the motifs table rows with results for the molecules which exhibit exhibited that type of particular issue will be displayed . Whenever you pick something in a drop down menu of the filter bar, the table. The number of motifs molecules that fit each your selection is given in brackets. If you want to make your selection even more specific, use the selection filed ''Id filter'' at the right of the filter bar.
Which table columns are filled depend mostly on Aside from its filtering function, the type of issue selected in the filter. The most important columns are ''Id'Details', ''Issues/Warnings'', ''Missing atoms/rings'', ''Atoms'', ''Processing warnings''also provides direct access to explicit validation reports for individual molecules. The other columns give additional information, usually helpful in identifying the source of the error in the structure. Note that complete structures '''do not''' contain columns with Just click on the information about missing atoms. The column Id refers to a (unique identifier assigned to each motif in order to keep a transparent trace of the motif's origin, as it contains containing the PDB ID, as well as the and a serial index of the first atom in the motif, as it appears in the original PDB entry. The column ''Issues/Warnings'' reports the number ) of issues or warnings found for each particular motif. The column ''Missing atoms/rings'' explains which atoms are missing in each validated motif, whereas ''Atoms'' shows the position molecule of incorrect chirality. ''Missing atoms'' are listed by their atom identifier interest in the model, whereas atoms with wrong chirality are listed by their identifier in the validated motif. Clicking on a column header allows order to sort the motifs according be redirected to the property specified in the headercorresponding validation report.
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==3D visualizationSingle molecule report==[[File:VDB_Details_entry.PNG|thumb|right|500px650px|'Detailed validation report for a '''single molecule''', accessible by clicking on the respective molecule Id in the '''Details''3D'table of the ''specifics page'' visualization . Consists of a full description for the molecule and detailed the model, complete with references, all resultsfrom all validation analyses, and 3D visualization of all structures involved in the validation process.]]
The 3D viewer implemented in the [[ValidatorDB]] interface '''single molecule report''' offers one step further in a complete image of the analysis of validation results for each individual validated motif, and particular molecule. It is accessible via the '''Details''' tab on the ''specifics page. In the table'', simply click by clicking on the Id (unique identifier containing the PDB ID and a serial number) of a motif the molecule of interest . As you open this report, the molecule Id will appear in order to open the top left corner of the report. The '''single molecule report''' starts with two 3D viewervisualizers, where you can inspect the structural inaccuracies more closely. Here you will be able to view and manipulate with the 3D representations of the validated molecule, the input motif , the model, and model residuesuperimpositions of these, in order to help you better assess the position and relevance of the structural issues found during validation(see the full list of terms [[ValidatorDB:Terminology | here]]). AdditionallyAt the top of each visualizer there is a drop down menu where you may choose the structure of interest, along with a few visualization options (atom labels, bonds vs sticks, full screen view). The 2D representation of the model is also provided for clarity, which and is especially helpful for larger motifsmolecules. Basic  Beneath the visualizers, the '''single molecule report''' is organized into three columns, but you may have to scroll down to see all the information about in each column. The left column contains the validated motif is also givenfull identification of the molecule in its original PDB entry, the description of the model and full identification in the wwPDB CCD, along with and a complete report list of [[ValidatorDB:Database_contents#Processing_warnings | processing warnings]], if any were encountered during validation. The middle column lists the validation resultsof the ''completeness'' and ''chirality'' analyses, where all and the right column those of the ''advanced'' analyses (see the potential issues full list of validation analyses [[ValidatorDB:Principles#Validation_analyses | here]]). Each problematic atom is listed. The results are listedlabeled 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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==Processing Warnings==
[[File:VDB_Warnings.PNG|thumb|right|500px650px|The '''Processing warnings''' tabof the ''specifics page'' lists unusual circumstances encountered during validation.]]
The validation reports in ValidatorDB ''specifics page'' may also mention various contain the separate tab '''Processing warnings''', which lists unusual aspects circumstances encountered during the validationof each molecule. Sometimes the processed PDB entries contain information that is ambiguous, conflicting or which deviates strongly from the expected reference. [[ValidatorDB]] reports such events as processing warnings. Such information can be found in the '''Processing Warnings''' tab on the specifics page. The selection field at the top of the page helps filter the warnings for different residues, in case more of them are in validation report. Simply click on the drop down menu and select the category of warnings that you would like to explore. Processing warnings are issues that may cause incorrect Validation, such as bad two residues being too close together (misused concept of alternate conformations) or unusual bond lengths given by the CONECT records. Make sure that negative validation results (e.g., missing atoms) are not in fact caused by ignoring some atoms in an ill-formed structure.
Overally a Some '''Processing warnings''' are issues that may cause incorrect validation, such as two molecules being too close together in the 3D space, or some atoms being too far (disconnected) from the rest of the molecule. Such structures are generally marked as ''degenerate'' in the ''completeness'' analyses. Other '''processing warning may simply lead warnings''' are only meant to ignoring a faulty atominform of which course of action was taken during validation (e.g., but which conformer was validated if several conformers of that molecule were present in the original PDB entry). The drop down menu at the top of the page helps filter the motif is validatedwarnings for molecules with a specific annotation (3-letter code).
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