MotiveValidator:Technical details

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Availability and technical details

Where to find MotiveValidator

MotiveValidator is freely available via the internet since September 2013 at our webpages. There is no login requirement for using MotiveValidator. If you find this tool useful for your work, please cite it as:[1]

What you need in order to run MotiveValidator

  • Up to date internet browser with WebGL support.
  • JavaScript enabled.

Check it out, if your browser is WebGL and Javascript compliant.

How to get around the web page

For the quick tour on using MotiveValidator service, please click the Guide button in the upper right corner and follow instructions.


Command line version

This is help for version 1.1.14.11.7c or newer. The help text for other versions be viewed using the --help command when running the application.

Running the Service

The service can be executed using the command (latest .NET Framework required):

WebChemistry.MotiveValidator.Service.exe workingFolder configuration.json

In Linux (where available) and MacOS, the latest version the Mono Framework (http://mono-project.com/) must be used to run the application:

mono WebChemistry.MotiveValidator.Service.exe workingFolder configuration.json


Configuration

The configuration is specified using the JSON format.

Configuration Example

This is the general shape of the JSON input configuration.

{
  "ValidationType": "Model",
  "InputFolder": "./MAN",
  "ModelsSource": "./MAN_Models",
  "IsModelsSourceComponentDictionary": false,
  "IgnoreObsoleteComponentDictionaryEntries": false,
  "SummaryOnly": false,
  "DatabaseModeMinModelAtomCount": 0,
  "DatabaseModeIgnoreNames": [],
  "MaxDegreeOfParallelism": 8
}

There has to be exactly one configuration file for each validation run. Every value, as well as settings' names, is surrounded in quotation marks (" " or ' '). Backslashes (\) have to be escaped (\\). File system paths can be absolute as well as relative (/ works as well in paths).

Attributes

Type of the validation.
  • InputFolder [ String ]
Folder with the input data. Each molecule to be validated has to be in a separate file. Supported file formats: *.pdb; *.pdbX, *.cif, *.pqr, *.mol. Gzip compression (*.gz) is also supported.
  • ModelsSource [ String ]
Folder or zip file with models in PDB (and SD/SDF/MOL for bonds) format. Alternatively, use the new PDB standard mmCIF (*.cif).
  • IsModelsSourceComponentDictionary [ Boolean ]
Determines if the ModelsSource is a CIF file containing models to be validated.
  • IgnoreObsoleteComponentDictionaryEntries [ Boolean ]
Determines if to ignore Component Dictionary entries with _chem_comp.pdbx_release_status = OBS flag.
  • SummaryOnly [ Boolean ], Default value = false
Determines whether to compute only the summary file and not files with motifs.
  • DatabaseModeMinModelAtomCount [ Int32 ]
Determines the minimum number of atoms a model needs to have.
  • DatabaseModeIgnoreNames [ String[] ]
Residues to ignore in the database mode.
  • MaxDegreeOfParallelism [ Int32 ], Default value = 8
Max degree of parallelism.

Descriptions

ValidationTypes
  • Model
Analyzes the input biomolecule fragments (motifs) against the provided model using the ModelFilename attribute.
  • Sugars
When running from the command line, identical to the CustomModels mode.
  • CustomModels
Automatically identifies and validates input models within the PDB structures.
  • Database
Special mode for creating ValidatorDB.
  • DatabaseCustom
Special mode for creating custom ValidatorDB analysis.

Output Description

General Structure

  • [WorkingDirectory] - Working directory of the application.
  • result - Contains the result of the computation.
log.txt - Contains the console output of the application.
status.json - Contains general information of the computation (running time, version, etc.).

MotiveValidator Specific Structure

  • result - Folder with computation result.
result.zip - A zip archive with compressed result.
result.csv - File that contains complete information about the result of validation of each motif in a compressed manner.
result.json - File that contains complete information about the result of validation of each motif, as well as list of warnings and errors, list of general errors, number of validated motifs, validation type and MotiveValidator version.
general_errors.csv - File that contains list of general errors.
  • [3-letter residue code] - A folder for each input model.
  • matched - Folder that contains pairs of validated motif and aligned model, both in PDB format.
  • mols - Folder that contains validated motifs in mol format.
  • motifs - Folder that contains validated motifs in PDB format.
  • notanalyzed - Folder that contains motifs that were not validated.
errors.csv - File that contains list of errors.
pairing.csv - File that contains pairing matrix of motifs' atoms versus model's atoms.
summary.json - File that contains rich summary of each single validation run.
[3-letter residue code]_model.mol - Mol file that contains the model.
[3-letter residue code]_model.pdb - PDB file that contains the model.
warnings.csv - File that contains list of warnings.

Specific File Descriptions

This section contains detailed descriptions of selected specific files.

index.csv

Contains complete information about the result of validation of each motif in a compressed manner.

The CSV file contains these columns:

  • ModelName [ String ]
Residue name of the model.
  • Id [ String ]
Name of the validated motif without extension.
  • State [ String ]
Validation state of the entry.
  • MainResidue [ String ]
Name and number of main residue of validated motif
  • ResidueCount [ Number ]
Number of residues present in validated motif file
  • Residues [ String ]
List of residues present in this motif file. List entries are separated by ;.
  • MissingAtomCount [ Number ]
Number of atoms that are lacking in validated motif.
  • MissingRingCount [ Number ]
Number of rings (chemical cycles) that are lacking in validated motif.
  • NameMismatchCount [ Number ]
Number of motif's atoms that are incorrectly named in the sense of alignment with the model.
  • ChiralityMismatchCount [ Number ]
Number of chiral atoms in validated motif that have different ligand position from the model.
  • SubstitutionCount [ Number ]
Number of atoms in validated motif that have been substituted with other element.
  • WrongBondCount [ Number ]
Number of wrong bonds.
  • BondDiscrepancy [ Number ]
Signals whether the matched motif bond(s) differ from the model ones.
  • MissingAtoms [ String ]
List of atoms from validated motif that are considered missing. Each entry of this list consists of atom name, atom element and index of atom from the model that does not have its counterpart in this motif.
  • MissingRings [ String ]
List of rings from validated motif that are considered missing. Each entry of this list consists of a sequence of atoms that comprise the missing ring and an integer that signifies number of missing rings of each composition (ex. CCCCO*1 means one missing ring of composition CCCCO).
  • NameMismatches [ String ]
List of atoms from this validated motif which have been paired to a differently named atoms from the model. Each entry of this list consists of motif atom specifications (name, element and index), a separator (->) and paired model atom specifications (name, element and index).
  • ForeignAtoms [ String ]
List of atoms in this validated motif that do not belong there. Each entry of this list consists of model atom specifications (name, element and index), a separator (->), paired motif atom specifications (name, element and index), separator (,) and specifications of the foreign atom (name, index and residue chain identifier).
  • Substitutions [ String ]
List of atoms with different element symbols from the model structure (ie. O substituted by N).
  • ChiralityMismatches [ String ]
List of chiral atoms from this validated motif that differ in spatial composition of connected atom(s) from paired chiral atoms of the model. Each entry of this list consists of model atom specifications (name, element and index), a separator (->) and paired motif atom specifications (name, element and index).
  • WrongBonds (ModelFrom-ModelTo:Motive:Exp/Got) [ String ]
Wrong Bonds. Currently unused.
  • ModelRmsd [ Number ]
Root mean square deviation of atomic positions (RMSD) value of the model-motif alignment.

index.json

File that contains complete information about the result of validation of each motif, as well as list of warnings and errors, list of general errors, number of validated motifs, validation type and MotiveValidator version. This file is used to display the data in the web UI.

In .NET languages, the file can be parsed into the type WebChemistry.MotiveValidator.DataModel.ValidationResult from the library WebChemistry.MotiveValidator.DataModel using the Newtonsoft.Json or similar library. Other straightforward analysis tool for this file is JavaScript (for example in browser or using Node.js).

References

  1. Vařeková,R.S., Jaiswal,D., Sehnal,D., Ionescu,C.-M., Geidl,S., Pravda,L., Horský,V., Wimmerová,M. and Koča,J. (2014) MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. Nucleic Acids Research, 42(Web Server issue), W227–33.


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