Prepare data for deposition with pdb_extract and SF-Tool
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. 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
SF-Tool is a streamlined, web-based tool for validating X-ray, neutron, and hybrid experimental data.
Visit sf-tool.rcsb.org to:
- 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@example.com 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, Bunkczi, 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.