arrow

From NeuroLex

Jump to: navigation, search



Resource:RCBS PDB Software Tools

Name: Resource:RCBS PDB Software Tools
Description: Software tools made available through the RCBS.

Data Extraction and Deposition Preparation Tools

  • pdb_extract (for workstation) - Tools and examples for extracting mmCIF data from structure determination applications
  • ADIT (for workstation) - A web-based package for preparing, editing and checking structure data entries

Data Format Conversion Tools

  • PDBML2CIF - A tool for converting PDBML data files into mmCIF data files
  • CIFTr - A tool for translating mmCIF data files into PDB format
  • MAXIT - An application for processing and annotating of macromolecular structure data
  • sf-convert - A format conversion tool for structure factor files that supports more than a dozen file formats
  • MMCIF Dictionary Suite - Collection of tools to parse, validate, manage data dictionaries used by the PDB. Applications are also included, which convert data dictionaries to XML schema, provide HTML browsing, produce mapping information for relational database loaders (Db Loader) and convert data files between related CIF dialects

Data Validation Tools

  • PDB Validation Suite - tools for processing and checking structure data

Data Parsing Tools

  • CIFPARSE-OBJ - A Class Library of Access Tools for mmCIF in C
  • CIFPARSE - A C Library of Access Tools for mmCIF in C (no longer maintained)
  • STAR (CIF) - Parser Several object-oriented Perl modules to parse mmCIF data files

Dictionary and Data Management Tools

  • DICT-OBJ-FILE - A Class Library of mmCIF Dictionary Access Tools (formerly known as CIFOBJ)
  • CIFTABLE (ISTable) - A Class Library of Table Access Tools for mmCIF data
  • Db Loader - An application to load mmCIF data into relational databases and XML (formerly known as mmcif-loader)

Other Software Tools

  • PointSuite – generate BIOMT and CIF symmetry records for macromolecular assemblies with point and helical symmetries
  • mmLIB - a Python macromolecular toolkit (including support for mmCIF)
  • BioPython - Python toolkit for computational biology (including support for mmCIF)
  • XML2PDB - an open-source C program for converting XML to PDB format
  • OOSTAR - Applications to Manipulate STAR Files (Objective-C)
  • OpenRasMol - Open source versions of RasMol (with CIF support)
  • CBFLib - A library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files
  • cif2pdb - Program to Convert mmCIF to pseudo-PDB Format
  • CIFtbx2 - Extended CIF Tool Box (Fortran) with CYCLOPS and cif2cif
  • pdb2cif - Scripts to Filter a PDB Entry and Produce mmCIF
  • CIFLIB - C Language Application Program Interface (no longer supported)
  • OpenMMS Toolkit - A suite of Java source code that includes an mmCIF parser, RDBMS loader, XML translator, and Corba server (no longer supported)
Parent Organization: Resource:PDB
Related to: Resource:Protein Data Bank Markup Language
Resource Type(s): Software resource
Abbreviation: RCSB Software Tools
Resource: Resource
URL: http://sw-tools.pdb.org/index.html
Id: nif-0000-31399
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Curated

For Resource Owners:

A sitemap will keep your NIF Registry description up-to-date and inform search engines about your resource.

Please login to create the sitemap. (top right)

Learn more about what NIF can do for your resource.
Proudly proclaim your inclusion in NIF by displaying the "Registered with NIF" button on your site.

Notes

This page uses this default form:Resource

Alt. URL: http://deposit.pdb.org/mmcif/FILM/

Contributors

Aarnaud



bookmark
Facts about Resource:RCBS PDB Software ToolsRDF feed
AbbrevRCSB Software Tools  +
CurationStatuscurated  +
DefiningCitationhttp://sw-tools.pdb.org/index.html  +
DefinitionSoftware tools made available through the Software tools made available through the RCBS.

Data Extraction and Deposition Preparation Tools

  • pdb_extract (for workstation) - Tools and examples for extracting mmCIF data from structure determination applications
  • ADIT (for workstation) - A web-based package for preparing, editing and checking structure data entries

Data Format Conversion Tools

  • PDBML2CIF - A tool for converting PDBML data files into mmCIF data files
  • CIFTr - A tool for translating mmCIF data files into PDB format
  • MAXIT - An application for processing and annotating of macromolecular structure data
  • sf-convert - A format conversion tool for structure factor files that supports more than a dozen file formats
  • MMCIF Dictionary Suite - Collection of tools to parse, validate, manage data dictionaries used by the PDB. Applications are also included, which convert data dictionaries to XML schema, provide HTML browsing, produce mapping information for relational database loaders (Db Loader) and convert data files between related CIF dialects

Data Validation Tools

  • PDB Validation Suite - tools for processing and checking structure data

Data Parsing Tools

  • CIFPARSE-OBJ - A Class Library of Access Tools for mmCIF in C
  • CIFPARSE - A C Library of Access Tools for mmCIF in C (no longer maintained)
  • STAR (CIF) - Parser Several object-oriented Perl modules to parse mmCIF data files

Dictionary and Data Management Tools

  • DICT-OBJ-FILE - A Class Library of mmCIF Dictionary Access Tools (formerly known as CIFOBJ)
  • CIFTABLE (ISTable) - A Class Library of Table Access Tools for mmCIF data
  • Db Loader - An application to load mmCIF data into relational databases and XML (formerly known as mmcif-loader)

Other Software Tools

  • PointSuite – generate BIOMT and CIF symmetry records for macromolecular assemblies with point and helical symmetries
  • mmLIB - a Python macromolecular toolkit (including support for mmCIF)
  • BioPython - Python toolkit for computational biology (including support for mmCIF)
  • XML2PDB - an open-source C program for converting XML to PDB format
  • OOSTAR - Applications to Manipulate STAR Files (Objective-C)
  • OpenRasMol - Open source versions of RasMol (with CIF support)
  • CBFLib - A library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files
  • cif2pdb - Program to Convert mmCIF to pseudo-PDB Format
  • CIFtbx2 - Extended CIF Tool Box (Fortran) with CYCLOPS and cif2cif
  • pdb2cif - Scripts to Filter a PDB Entry and Produce mmCIF
  • CIFLIB - C Language Application Program Interface (no longer supported)
  • OpenMMS Toolkit - A suite of Java source code that includes an mmCIF parser, RDBMS loader, XML translator, and Corba server (no longer supported)
    d Corba server (no longer supported)
Has default formThis property is a special property in this wiki.Resource  +
Has roleSoftware resource  +
Idnif-0000-31399  +
Is part ofResource:PDB  +
LabelResource:RCBS PDB Software Tools  +
ModifiedDate21 December 2012  +
Page has default formThis property is a special property in this wiki.Resource  +
RelatedToResource:Protein Data Bank Markup Language  +
SuperCategoryResource  +