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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===
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]]''.
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|<!--Col1-->The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. The support tab '''Quick Help''' helps you get started, with basic information about how to get oriented in the web page. Various interactive guides are accessible by a green button at the top right corner of some tabs. Tool tips are available for most of the graphical elements.
|<!--Col2--> The '''Samples''' tab offers basic examples of database snippets, along with a 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 more complex analyses are available as ''[[ValidatorDB:CaseStudies | case studies]]''.
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The '''ValidatorDB''' synopsis page further provides access to various data sets of . You may retrieve specific validation reports using the '''[[ValidatorDB:Database_organization#Search | Search]]''' tab. Further, the results from PDB-wide validations are available via four three different tabs, namely '''[[ValidatorDB:Database_organization#Overview | Overview]]''', '''[[ValidatorDB:Database_organization#Details_by_molecule | Details by Residuemolecule]]''', and '''[[ValidatorDB:Database_organization#Details_by_PDB_entry | Details by PDB entry''' and '''Custom Search]]'''. A full description of each of these tab is given in their respective sections.
Additionally, the ''synopsis page'' allows to access the validation results for specific residues of interest via the '''Quick Lookup bar''' at the bottom of the page. Simply type a comma separated list of residue annotations (3-letter codes) into the '''Quick Lookup bar''', and you will be redirected to the [[ValidatorDB:Database_organization#Specifics_page | specifics page]] containing validation results for the molecules you requested. If you specify a list of PDB IDs (4-letter codes) instead, then the corresponding [[ValidatorDB:Database_organization#Specifics_page | specifics page]] will contain validation results for all relevant molecules in the PDB entries you specified.
==Search==Overview====[[File:VDB_overview.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.]]
[[File:ValidatorDB-Search By Entry and Annotation.png|thumb|right|650px|The Overview '''Search tab of the synopsis page provides ''' allows to 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 very general statistical evaluation combination of results across the entire PDB in graphical form. The elements of the graph represent percentages of the total number of motifs entry and molecule annotation (over 200,000shown here) of residues relevant for validation. A graphic element In each case you will be displayed in the '''Overview''' graph only if it represents at least 0.5% provided with an input field, where you can enter a list of values for the total number of motifsrelevant criterion. Each element of the graph is described in a Examples and tool tip, but note that here tips are provided for easy reference with respect to the term residue actually refers to occurrence of residue (motif)expected syntax.]]
The elements of '''ValidatorDB''' contains validation results for the graph can be assigned to roughly 6 categories, depending on which kind entire Protein Data Bank. You are probably interested only in a subset of information they contain these (e.g., incomplete residue, chirality issues, warnings, etcthe validation results for a specific inhibitor which appears in the PDB entry you plan to use further in your simulations). The categories are marked by different colors. All ''synopsis page'' allows to access specific validation reports via the graph elements are explained in the [[ValidatorDB:Analysis_of_Results| results section]]'''Search tab'''.
Note that this table can be downloaded in 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 PDB entry and molecule annotation.csv format after clicking 'CSV' in The syntax of the bottom right corner of search is quite simple, but you can always check out the infographicsexamples and tool tips if you want to make sure.
====Details by molecule====Click on criterion you plan to use. In each case, there will be an input field where you can enter a comma or new line separated list of 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 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 '''ValidatorDB''', organized and made accessible via a unique ''[[FileValidatorDB:VDB_Residues.PNGDatabase_organization#Specifics_page |thumb|right|500px|The ''synopsis specifics page]]'' consists of 6 tabs, two providing support, and four enabling which you can access to the database itselfat a later time via its unique URL. The support tabs '''Quick Help[[ValidatorDB:Database_organization#Specifics_page | specifics page]]''is described in detail in the second part of the ' and 'Data organization''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 section of some tabsthis manual.]]
The last 10 searches you performed are listed for your convenience.
The '''Details by Residue''' tab contains an interactive table summarizing the results for each residue validated across the entire PDB. 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).
<br style="clear:both" /> ==Overview==[[File:VDB_overview.png|thumb|right|650px|The table is interactive'''Overview tab''' contains an overall validation report for all the ligands and non-standard residues in the Protein Data Bank. Each bar represents overall statistics for the [[ValidatorDB:Database_contents | results ]] of a certain type of [[ValidatorDB:Principles#Validation_analyses | validation analysis ]]. Clicking on any element ]] 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 table header allows 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 sort the table entries according to that elementnumber 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. Click on any residue name A bar appears in order to access the '''ValidatorDBOverview''' specifics page with detailed validation 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 that residuedifferent 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>.  <br style="clear:both" />
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.==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 entry====-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.
[[File:VDB_PDBEntries.PNG|thumb|right|500px|The ''synopsis page'' consists table is interactive, allowing efficient sorting and filtering of 6 tabs, two providing supportthe results, and four enabling direct access to more detailed validation reports for the database itselfentries of interest. By default, only the results of some analyses are included in the table. The support tabs complete list of analyses available in '''Quick HelpValidatorDB''' and '''Samples''' help you get started, with basic information and examples of database snippetsis given below the table. Various interactive guides are accessible You may customize the table by adding or removing columns which refer to a green button 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 of some tabsallows to retrieve only the results for molecules with certain annotations. Regular expressions may be used.]]
The '''Details by PDB Entry''' tab contains an interactive table summarizing the results for all residues validated in each PDB entry. Each row corresponds to one PDB entry, identified by its PDB ID Click on any molecule annotation (43-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.
The table is interactive. Clicking on any element in Results can be interpreted using the table header allows to sort the table entries according to that element. Click on any PDB information in order to access the '''[[ValidatorDB:Specifics_pageDatabase_contents | ValidatorDB specifics pageDatabase contents]]''' with detailed validation results . Tool tips are available for all residues in that PDB entryeach element of the table header.
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 for different types of validation analyses are labeled using the download button at the top left cornerunified 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>.<br style="clear:both" />
==Details by PDB entry==
====Custom search====[[File:VDB_PDBEntries.PNG|thumb|right|650px|The '''Details by PDB entry''' 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 relevant molecules in a single PDB entry. For a given PDB entry, 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 ]].]]
[[File:VDB_Custom.PNG|thumb|right|500px|The ''synopsis page'Details by PDB Entry' consists '' tab contains an interactive table summarizing the results for sets of 6 tabsmolecules sharing the same PDB entry. Each row corresponds to one PDB entry, two providing supportidentified by its PDB ID (4-letter code). For a given PDB entry, and four enabling access each column refers to the database itselfresults from a specific validation analysis. The support tabs '''Quick Help''' and '''Samples''' help you get startedEach cell gives the number (or percentage) of molecules which exhibited issues (missing atoms, wrong chirality, etc.), or fared well (complete structure, correct chirality, with basic information and examples of database snippetsetc. Various interactive guides are accessible by ) during a green button at the top right corner of some tabsgiven 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 '''Custom SearchValidatorDB''' tab 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 you to create your own view of sort the table entries according to that element. The filter at the ligands validation of top right corner allows to retrieve only the PDB database. Simply paste a list of your desired ligands results for molecules with certain annotations (3-letter codecodes) and/, or originating from PDB entries with certain PDB IDs (4-letter codecodes) in provided text boxes separated by commas or a newlines. This is particularly convenient Regular expressions may be used. Click on any PDB entry in case you need order to retrieve a validation report for a huge number of structures. Such as all access the ''glycosyltransferases'ValidatorDB''' or ''nmr structuresspecifics page''with detailed validation results for all molecules in that specific PDB entry. Note that you  Results can retrieve such lists by be interpreted using the information in the [[httpValidatorDB://wwwDatabase_contents | Database contents]].rcsbTool tips are available for each element of the table header.org The results for different types of validation analyses are labeled using the unified color scheme: <span style="color:#006400">complete structure and correct chirality</pdbspan>, <span style="color:#FF0000">incomplete structure</searchspan>, <span style="color:#DAA520">wrong chirality</advSearch.do advanced search in PDB]. Also bear in mind that each of these custom searches will be assigned a unique permanent web addressspan>, so you can access these results later on. Also a list of your last custom searches is provided for your convenient<span style="color:#607d8b">warning</span><br style="clear:both" />
=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==
[[File:VDB_Residue_summary.PNG|thumb|right|500px|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.
On the '''{| class="wikitable" border="1" style="margin: 1em auto 1em auto;" |- |<!--Col1-->[[File:VDB_Residue_summary.PNG| 650px]] |<!--Col2-->[[ValidatorDBFile:VDB_Entry_summary.PNG| 650px]] |- |<!--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, the first view a recapitulation of the results is available in the 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''' tabof the ''specifics page'' for a '''single PDB entry''' allows easy navigation between annotation-based<br/> validation reports. For 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 validated residuevalidation analysis<br/> (completeness, chirality, advanced), the Summary tab provides an overview of potential issues encounteredand statistics for each problematic atom. |}
If more than one residue were validated in one runFirst, the model from wwPDB CCD is briefly described by name, molecular formula, 2D structure, etc. Next, a list recapitulation of these residues will be at the top all molecules and their respective PDB entries is also included, followed by a table with results of the pagemain validation analyses (completeness, chirality, advanced). In order to examine the For each validation summary analysis, statistics are provided for each residue, you will need to either click on all problematic atoms. Note that specific residue in here the list, or just scroll down statistics cover only the page till you reach it. Each validated residue is identified by its molecules sharing this annotation (3-letter code, as well as its chemical formula and common name. Validation statistics are given as absolute numbers and percentages over all the motifs that were processed for each residue).
The first table with the validation report results is organized into two main sections, referring to '''incomplete''' (''Missing Atoms'' or ''Rings'') and ''complete structures''. respectively. The section with ''complete structures''is further organized into subsections based on the results of the ' (''With All Atomschirality'' and ''Ringsadvanced'') respectivelyanalyses. The formal Specifically, a general distinction is made between ring atoms ''complete structures'' with ''correct chirality'' and non-ring atoms (simply denoted as atoms) is meant to allow a quick localization of potential issues in residues containing rings, especially where with ''wrong chirality''. Warnings like ''foreign atom identifiers are not useful. ''and 'Chirality'substitutions'' 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 highlighted, in order to better localize the problems in the structuresalso included.
LastSubsequent tables highlight problematic atoms and provide useful statistics, a 2D representation of in order to better localize the problems in the model residuestructures. If you click on any validation issue (e.g., and missing rings, wrong chirality on a pie chart specific atom), you will be redirected to the '''Details''' tab where only the molecules with the validation results those specific issues are provided for visual representation purposeslisted. You  Results can download them via be interpreted using the small icon at information in the top right corner [[ValidatorDB:Database_contents | Database contents]]. Tool tips are available for each element of the charttable headers. 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>, and later use them in your presentations<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''' table of the ''specifics page''. Consists of a full description for the molecule and the model, complete with references, all results from all validation analyses, and 3Dvisualization of all structures involved in the validation process.]] The '''single molecule report''' offers a complete image of the validation results for each particular molecule. It is accessible via the ''' visualization Details''' tab on the ''specifics page'', by clicking on the Id (unique identifier containing the PDB ID and a serial number) of the molecule of interest. As you open this report, the molecule Id will appear in the top left corner of the report. The '''single molecule report''' starts with two 3D visualizers, where you can manipulate with the 3D representations of the validated molecule, the input motif, the model, and superimpositions of these, in order to better assess the position and detailed resultsrelevance of the structural issues found during validation (see the full list of terms [[ValidatorDB:Terminology | here]]). At 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, and is especially helpful for larger molecules.
The 3D viewer implemented in Beneath the [[ValidatorDB]] interface offers one step further in the analysis of each individual validated motifvisualizers, and is accessible via the '''Detailssingle molecule report''' tab on is organized into three columns, but you may have to scroll down to see all the specifics pageinformation in each column. In The left column contains the full identification of the tablemolecule in its original PDB entry, simply click on the Id description of the model and full identification in the wwPDB CCD, and a motif list of interest in order to open the 3D viewer[[ValidatorDB:Database_contents#Processing_warnings | processing warnings]], where you can inspect the structural inaccuracies more closelyif any were encountered during validation. Here you will be able to view and manipulate with The middle column lists the 3D representations results of the validated motif ''completeness'' and model residue''chirality'' analyses, to help you better assess and the position and relevance right column those of the structural issues found during ''advanced'' analyses (see the full list of validationanalyses [[ValidatorDB:Principles#Validation_analyses | here]]). Additionally, a 2D representation of the model Each problematic atom is provided for clarity, which is especially helpful for larger motifslisted. Basic information about The results are labeled using the validated motif is also givenunified color scheme: <span style="color:#006400">complete structure and correct chirality</span>, <span style="color:#FF0000">incomplete structure</span>, along with a complete report of the validation results<span style="color:#DAA520">wrong chirality</span>, where all the potential issues are listed<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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