New pdb_extract Release

08/23

pdb_extract.

Version V3.11 of pdb_extract has been released as an online web tool and a downloadable workstation program.

pdb_extract is a program that minimizes errors and saves time during the deposition process by extracting key details from the output files produced by many X-ray crystallographic and NMR applications. The program merges these data into macromolecular Crystallographic Information File (mmCIF) data files that can be used with ADIT for validation and deposition.

New features include:

• Data from hybrid method experiments
• NCS and TLS ranges in BUSTER and REFMAC
• Improved mtz to mmCIF conversion
• Quality assessment of X-ray data

Complete details are available in the release notes and manual.

Depositors can upload files into the pdb_extract webserver or download the latest workstation version at pdb-extract.rcsb.org. Tutorials are also available for X-ray and NMR.

News Index

• 12/27 Happy Holidays

• 12/20 Notice for REFMAC Users

• 12/13 Looking for Ligands

• 12/13 Paper Published

• 12/06 Latest Website Release

• 11/29 Search the PDB for homo- and hetero-multimer structures

• 11/22 Customize Your RCSB PDB Homepage

• 11/15 Molecule of the Month News

• 11/08 Use the Top Bar Suggestion Box for Quick and Precise Searching

• 11/01 New Target Registration Database

• 10/25 PDB40 Symposium

• 10/18 Newsletter published

• 10/11 Educational Resources for Mobile Devices

• 10/04 PDB Pioneers

• 09/27 Poster Prize Awarded at IUCr

• 09/20 New Structures Widget

• 09/13 Latest Website Release

• 09/06 Tools for Education

• 08/30 Validate Structure Factor Diffraction Data with SF-Tool

• 08/23 New pdb_extract Release

• 08/16 RCSB PDB Poster Prize at IUCr

• 08/16 wwPDB Events at IUCr (August 22-30, 2011)

• 08/09 Poster Prize Awarded at ISMB

• 08/02 Different Ways To Explore New Entries

• 08/02 PDB40 Abstracts Due August 15

• 07/26 Analyze small molecule interactions in the PDB with Ligand Explorer

• 07/26 Travel Award Applications for PDB40 due August 1

• 07/19 Protein Society Meeting

• 07/19 Travel Award Applications for PDB40 due August 1

• 07/12 ISMB and 3DSIG Meetings

• 07/05 Newsletter published

• 06/28 Browse Membrane Transport Proteins

• 06/21 Build complex queries with Advanced Search

• 06/14 Poster Prize Awarded at ACA

• 06/07 Browse the PDB by GO Terms, EC Number, Source Organism, and More

• 05/31 Enhanced Sequence Display

• 05/24 Upcoming Meeting: ACA

• 05/17 Validate Entries Before Deposition

• 05/10 Educational Resources to Explore a Structural View of Biology

• 05/03 Newsletter published

• 04/26 New Publication

• 04/26 Rutgers Day (April 30)

• 04/19 Latest Website Release

• 04/12 DNA Day 2011: April 15

• 04/12 Narrated RCSB PDB Tutorial Updated

• 04/05 J.P. Stevens HS Wins NJ Protein Modeling Event

• 03/29 The Structural Biology of HIV

• 03/22 Quick Jmol Views

• 03/15 Visit us at the San Diego Science Festival on March 26

• 03/15 Paper Published

• 03/08 Depositing Structures with Ligands

• 03/01 Upcoming Meetings

• 02/22 Structural Neighbors

• 02/15 Upcoming Meeting: AAAS Meeting and Family Days

• 02/08 Create High Resolution Images

• 02/01 Store Personal Annotations With MyPDB

• 01/25 NJ Science Olympiad Protein Modeling Results

• 01/18 Newsletter published

• 01/11 Papers Published

• 01/04 Structural Biology Knowledgebase Widget