New Release of pdb_extract Available Online and for Download

07/20

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.

Version V3.10 of pdb_extract has been released, and provides:

• Support for several new versions of programs (including REFMAC version 5.5 and higher), for a total of 37 programs/packages with hundreds of different formats
•  Improved extraction and parsing from programs (e.g., PHENIX version 1.4 and later, BUSTER-TNT version 2.8 & higher) and log files (MLPHARE)
• Support for multiple MTZ file conversion

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

News Index

• 12/28 Happy Holidays

• 12/21 Deposition Session Restart IDs

• 12/14 Annual Report Published

• 12/07 Poster Prize Awarded at AsCA

• 12/07 Latest Website Release

• 11/30 Learn About Viruses

• 11/30 New and Improved Web Services for Accessing PDB Data

• 11/23 New Ligand Summary Pages

• 11/16 Explore Search Results Using Data Distribution Summaries

• 11/09 Creating Tabular Reports

• 11/02 PDBMobile

• 10/26 Newsletter Published

• 10/19 Binding Affinity Data Integrated with RCSB PDB

• 10/12 Categorized View of Molecule of the Month

• 10/05 Latest Website Release

• 09/28 Poster Prize Awarded at ECM

• 09/28 Analyze small molecule interactions in the PDB with Ligand Explorer

• 09/21 Redesigned BioSync

• 09/14 Exploring Search Results

• 09/07 Tools for Education

• 08/31 Newsletter Published

• 08/24 New Flyers Available

• 08/24 Poster Prize Awarded at ACA

• 08/17 Upcoming Meeting: PDB Symposium at ACS

• 08/10 wwPDB News: Validation Report PDFs

• 08/10 ADIT 2.0 Offers Improved Deposition Process

• 08/03 Poster Prize Awarded at ISMB

• 07/27 Looking at Structures: A Resource for Learning About PDB Data

• 07/27 Paper Published

• 07/20 Upcoming Meeting: ACA

• 07/20 New Release of pdb_extract Available Online and for Download

• 07/13 Get the Latest wwPDB News

• 07/06 Improved Version of ADIT Available

• 07/06 ISMB and 3DSIG Meetings

• 06/29 Version 2 NMR Restraint Files Available from the wwPDB FTP

• 06/29 Use Ligand Expo When Depositing Structures with Ligands

• 06/22 Latest Structures Widget

• 06/15 Papers published

• 06/08 Improved Version of ADIT Available, Transitional Implementation Starts June 14

• 06/08 New Website Features

• 06/01 Create a Collage of Structures

• 05/25 Search the RCSB PDB in Your Web Browser

• 05/18 Turn Your Computer into a PDB Structure Kiosk

• 05/11 New Website Features and Widgets

• 05/04 Version 2 NMR Restraint Files to be Released in the wwPDB FTP on June 30, 2010

• 05/04 wwPDB To Provide Validation Reports as PDFs

• 04/27 Newsletter Published

• 04/20 Screencasts Demonstrate RCSB PDB Features

• 04/20 DNA Day: April 23

• 04/13 Come build virus models at Rutgers Day (April 24)

• 04/13 Exhibiting at Experimental Biology (April 24-28)

• 04/06 Bookmark and Share RCSB PDB Webpages

• 03/30 Advanced Search: Sequence Motif

• 03/23 West Windsor Plainsboro High School North Wins New Jersey Science Olympiad Protein Modeling State Finals

• 03/23 San Diego Science Festival Expo Day: March 27

• 03/16 Exhibiting at NSTA

• 03/09 Improved Ligand Searching

• 03/02 New Website Features

• 02/23 Changes to the wwPDB Policy for Depositing Polypeptide Structures

• 02/23 Online Narrated Tutorial Demonstrates How to Use the RCSB PDB

• 02/16 Exhibition at the Biophysical Society Meeting

• 02/09 Poster Download: How Do Drugs Work?

• 02/02 wwPDB FTP Advisory Notice

• 02/02 Newsletter Published

• 01/26 Comparison Tool for Exploring Sequence and Structure Alignments

• 01/19 NJ Science Olympiad Protein Modeling Results

• 01/12 Time-stamped Copies of PDB Archive Available via FTP

• 01/05 2009 Annual Report Published