Prepare data for deposition with pdb_extract and SF-Tool

07/31

(Click image to enlarge)
Image created at www.wordle.net.

Tools are available to help prepare data files for deposition with ADIT. Using these resources can help minimize errors, validate data, and save time during the deposition process.

pdb_extract extracts key details from the output files produced by many X-ray crystallographic and NMR applications.

pdb_extract extracts key details from the output files produced by many X-ray crystallographic and NMR applications. The program merges these data into mmCIF data files that can be used with ADIT for validation and deposition.

Features include support for:

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

Depositors can upload files into the pdb_extract webserver or download the latest workstation version at pdb-extract.rcsb.org.  

SF-Tool is a streamlined, web-based tool for validating X-ray, neutron, and hybrid experimental data.

Visit sf-tool.rcsb.org to:

(Click image to enlarge)
SF-Tool is a streamlined, web-based tool for validating X-ray, neutron, and hybrid experimental data.

• Validate model coordinates against structure factor data
• Easily convert structure factor files between different formats mmCIF, MTZ, CNS/CNX, XPLOR, SHELX, TNT, HKL2000, SCALEPACK, D*Trek, SAINT, and more)
• Check for and validate twinned or detwinned data

The latest release of SF-Tool includes support for neutron and hybrid experiments; incorporates checks from REFMAC¹, PHENIX², and SFCHECK;³ and
converts multiple data sets into a single mmCIF file.

Depositors can upload files into the pdb_extract webserver or download the latest workstation version at pdb-extract.rcsb.org.  

Contact [email protected] with any questions about these resources.

¹Refinement of Macromolecular Structures by the Maximum-Likelihood Method (1997) Murshudov, Vaguine, Dodson Acta Cryst. D53:240.
²PHENIX: a comprehensive Python-based system for macromolecular structure solution. Adams, Afonine, Bunkczi, et al. (2010) Acta Cryst. D66:213.
³SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structurefactor data and their agreement with the atomic model (1999) Vaguine, Richelle, Wodak Acta Cryst. D55:191.

News Index

• 12/25 Happy Holidays

• 12/18 Join the RCSB PDB Team

• 12/18 Papers Published

• 12/11 Announcement: Meeting on Hybrid Methods

• 12/11 Map PDB Structures to Full-length Protein Sequences

• 12/04 Advanced Search: Multiple ID Search

• 11/27 World AIDS Day: December 1

• 11/27 MyPDB: Keep up-to-date with new structures... automatically!

• 11/20 Take our quick survey

• 11/20 Educational Activities and Lessons

• 11/13 Ligand Searching

• 11/13 Take our quick survey

• 11/06 Explore Gallery View of Search Results

• 10/30 Improved Drug Searches and Annotations

• 10/23 New Website Release

• 10/16 Explore the Structural Biology of HIV

• 10/16 Nobel Prize Awarded for studies of G-protein-coupled receptors

• 10/09 Fall Newsletter Published

• 10/02 Turn Your Computer into a PDB Structure Kiosk

• 10/02 Advanced Search: Sequence Motif

• 09/25 Explore PDB Data Overviews

• 09/18 High Resolution Images at the RCSB PDB

• 09/11 Poster Prize Awarded at ECM

• 09/11 Customized Home Page: Structure Comparison Tool

• 09/04 Head Back to School with PDB-101

• 08/28 Smart Searching with the Top Bar Suggestion Box

• 08/21 Poster Prize Awarded at ACA

• 08/21 Download RCSB PDB Mobile for the iPhone/iPad

• 08/14 Poster Prize Awarded at ISMB

• 08/14 Improved Ligand Reports

• 08/07 Build complex queries with Advanced Search

• 07/31 Protein Society Annual Symposium

• 07/31 Prepare data for deposition with pdb_extract and SF-Tool

• 07/24 Upcoming Meeting: ACA

• 07/17 Different Ways To Explore New Entries

• 07/10 ISMB and 3DSIG Meetings

• 07/10 Summer Newsletter Published

• 07/03 Author Profiles: Timeline Display of a Researcher's Structures

• 06/26 Latest Website Release

• 06/19 National Protein Modeling Champions

• 06/19 Personalize the RCSB PDB with MyPDB

• 06/12 Top Bar SMILES String Searching

• 06/05 Molecule of the Month reaches 150

• 05/29 Tour the PDB with Drill-down Pie Charts

• 05/22 Domain-based Structural Alignments

• 05/15 New Poster: Virus Structures

• 05/08 Customized Home Page: Sequence Search

• 05/08 Bookmark and Post Webpages

• 05/01 Latest Website Release

• 04/24 Create a Collage of Structures

• 04/24 Rutgers Day (April 28)

• 04/17 Exhibiting at Experimental Biology

• 04/17 DNA Day 2012: April 20

• 04/10 Spring Newsletter Published

• 04/03 Depositing Structures with Ligands

• 03/27 Browse the PDB by GO Terms, EC Number, Source Organism, and More

• 03/20 J.P. Stevens HS Wins NJ Protein Modeling Event

• 03/20 Visit the San Diego Festival of Science and Engineering on March 24

• 03/13 PDBMobile and iOS 5.1

• 03/13 Preview New 3D Similarity Tab

• 03/13 Sound Science

• 03/06 Explore a Structural View of Biology at PDB-101

• 02/28 Visualize Molecular Surfaces with Protein Workshop

• 02/21 New Structures Widget

• 02/21 Visit the Biomolecular Discovery Dome at Biophysical Society

• 02/14 Ligand Summary Pages

• 02/07 Free Webinar and Updated Tutorial

• 02/07 Volunteer Structures For Foldit

• 01/31 Free Webinar on How to use the RCSB PDB

• 01/31 Announcement: Meeting on Hybrid Methods

• 01/24 Newsletter Published

• 01/17 NJ Science Olympiad Protein Modeling Results

• 01/10 Web Services for Accessing PDB Data

• 01/03 Annual Report Published