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Prepare data for deposition with pdb_extract and SF-Tool

07/31

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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.

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:

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

(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¬Ěczi, 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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