Difference between revisions of "ValidatorDB:UserManual"

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'''ValidatorDB''' is a database of precomputed validation results for all ligands and non-standard residues in the Protein Data Bank (PDB). The molecules deemed relevant for validation are all ligands and non-standard residues with 7 or more heavy atoms. Standard nucleotides, standard amino acids and selenomethionine are not covered. The models from the wwPDB Chemical Component Dictionary (wwPDB CCD) are used as reference structures during validation. The database is updated on a weekly basis.
 
'''ValidatorDB''' is a database of precomputed validation results for all ligands and non-standard residues in the Protein Data Bank (PDB). The molecules deemed relevant for validation are all ligands and non-standard residues with 7 or more heavy atoms. Standard nucleotides, standard amino acids and selenomethionine are not covered. The models from the wwPDB Chemical Component Dictionary (wwPDB CCD) are used as reference structures during validation. The database is updated on a weekly basis.
  
Below you can find all the information you need in order to make efficient use of '''ValidatorDB'''.  
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Below you can find the '''ValidatorDB''' user manual, which contains all the information you need in order to make efficient use of '''ValidatorDB'''. Additional support is provided on the '''ValidatorDB''' web pages. When you first access the '''ValidatorDB''' page, you will find basic information in the '''Quick Help''' tab, and useful examples of database snippets in the '''Samples''' tab. Moreover, various interactive guides are accessible at all times by a green button at the top right corner of some tabs. We recommend that you make use of these as often as you need.
  
===[http://www.slideshare.net/lukypravda/validatordb-first-time-user-guide-37728902 Introduction to ValidatorDB]===
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===[http://www.slideshare.net/lukypravda/validatordb-first-time-user-guide-37728902 First time user guide to ValidatorDB]===
 
If you are a first time user, we recommend that you go through the basic presentation specifically prepared to help you get oriented.
 
If you are a first time user, we recommend that you go through the basic presentation specifically prepared to help you get oriented.
  
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----
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===[[ValidatorDB:Introduction | Introduction]]===
 
----
 
----
  
 
===[[ValidatorDB:Terminology | Terminology]]===
 
===[[ValidatorDB:Terminology | Terminology]]===
Definitions of terms used in '''ValidatorDB'''
 
 
* [[ValidatorDB:Terminology#Residue | Residue ]]
 
* [[ValidatorDB:Terminology#Residue | Residue ]]
 
* [[ValidatorDB:Terminology#Non-standard_residue | Non-standard residue ]]
 
* [[ValidatorDB:Terminology#Non-standard_residue | Non-standard residue ]]
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* [[ValidatorDB:Terminology#Molecule | Molecule ]]
 
* [[ValidatorDB:Terminology#Molecule | Molecule ]]
 
* [[ValidatorDB:Terminology#Model | Model ]]
 
* [[ValidatorDB:Terminology#Model | Model ]]
* [[ValidatorDB:Terminology#Motif | Motif ]]
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* [[ValidatorDB:Terminology#Input_motif | Input motif ]]
  
 
===[[ValidatorDB:Principles | Principles]]===
 
===[[ValidatorDB:Principles | Principles]]===
Ddescriptions of principles used in '''ValidatorDB'''
 
 
* [[ValidatorDB:Principles#Validation_procedure | Validation procedure ]]
 
* [[ValidatorDB:Principles#Validation_procedure | Validation procedure ]]
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* [[ValidatorDB:Principles#Validation_analyses | Validation analyses ]]
 
* [[ValidatorDB:Principles#Validation_results | Validation results ]]
 
* [[ValidatorDB:Principles#Validation_results | Validation results ]]
 
* [[ValidatorDB:Principles#Validation_reports | Validation reports ]]
 
* [[ValidatorDB:Principles#Validation_reports | Validation reports ]]
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----
 
----
  
===[[ValidatorDB | Synopsis Page]]===  
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===[[ValidatorDB:Database_contents | Database contents]]===
PDB-wide statistics and custom validation reports
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# [[ValidatorDB:Database_contents#Incomplete_structures | Incomplete structures ]]
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# [[ValidatorDB:Database_contents#Complete_structures | Complete structures ]]
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## [[ValidatorDB:Database_contents#Wrong_chirality | Wrong chirality ]]
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## [[ValidatorDB:Database_contents#Correct_chirality | Correct chirality ]]
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# [[ValidatorDB:Database_contents#Warnings | Warnings ]]
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# [[ValidatorDB:Database_contents#Processing_warnings | Processing warnings ]]
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----
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===[[ValidatorDB:Database_organization | Database organization]]===
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# [[ValidatorDB:Database_organization#Synopsis_page | Synopsis page ]]
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## [[ValidatorDB:Database_organization#Search | Search ]]
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## [[ValidatorDB:Database_organization#Overview | Overview ]]
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## [[ValidatorDB:Database_organization#Details_by_molecule | Details by molecule ]]
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## [[ValidatorDB:Database_organization#Details_by_PDB_entry | Details by PDB entry ]]
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# [[ValidatorDB:Database_organization#Specifics_page | Specifics page ]]
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## [[ValidatorDB:Database_organization#Overview_2 | Overview ]]
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## [[ValidatorDB:Database_organization#Summary | Summary ]]
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## [[ValidatorDB:Database_organization#Details | Details ]]
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## [[ValidatorDB:Database_organization#Single_molecule_report | Single molecule report ]]
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## [[ValidatorDB:Database_organization#Processing_warnings | Processing warnings ]]
 +
----
  
===[[ValidatorDB:Analysis_of_Results | Specifics Page]]===
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===[[ValidatorDB:Limitations| Limitations]]===
Detailed validation reports for specific sections of the database
 
  
 
----
 
----
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===[[ValidatorDB:CaseStudies | Case studies]]===
  
===[[ValidatorDB:CaseStudies | Case Studies]]===
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----
Examples of interesting database snippets
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===[[ValidatorDB:Plugin | Molecular browsers extension ]]===
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# [[ValidatorDB:Plugin#Installation#PyMOL | PyMOL ]]
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# [[ValidatorDB:Plugin#Installation#Chimera | Chimera ]]
  
===[[ValidatorDB:UI | UI Description]]===
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----
Organization of the user interface
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===[[ValidatorDB:Technical_details | Technical details ]]===

Latest revision as of 18:20, 19 July 2017


ValidatorDB is a database of precomputed validation results for all ligands and non-standard residues in the Protein Data Bank (PDB). The molecules deemed relevant for validation are all ligands and non-standard residues with 7 or more heavy atoms. Standard nucleotides, standard amino acids and selenomethionine are not covered. The models from the wwPDB Chemical Component Dictionary (wwPDB CCD) are used as reference structures during validation. The database is updated on a weekly basis.

Below you can find the ValidatorDB user manual, which contains all the information you need in order to make efficient use of ValidatorDB. Additional support is provided on the ValidatorDB web pages. When you first access the ValidatorDB page, you will find basic information in the Quick Help tab, and useful examples of database snippets in the Samples tab. Moreover, various interactive guides are accessible at all times by a green button at the top right corner of some tabs. We recommend that you make use of these as often as you need.

First time user guide to ValidatorDB

If you are a first time user, we recommend that you go through the basic presentation specifically prepared to help you get oriented.


Introduction


Terminology

Principles


Database contents

  1. Incomplete structures
  2. Complete structures
    1. Wrong chirality
    2. Correct chirality
  3. Warnings
  4. Processing warnings

Database organization

  1. Synopsis page
    1. Search
    2. Overview
    3. Details by molecule
    4. Details by PDB entry
  2. Specifics page
    1. Overview
    2. Summary
    3. Details
    4. Single molecule report
    5. Processing warnings

Limitations


Case studies


Molecular browsers extension

  1. PyMOL
  2. Chimera

Technical details