Prepare data for deposition with pdb_extract and SF-Tool

07/31

(Click image to enlarge)
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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 deposit@deposit.rcsb.org 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.

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