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PDB2INS: bridging the gap between small-molecule and macromolecular refinement

The open-source Python program PDB2INS is designed to prepare a .ins file for refinement with SHELXL [Sheldrick (2015). Acta Cryst. C71, 3–8], taking atom coordinates and other information from a Protein Data Bank (PDB)-format file. If PDB2INS is provided with a four-character PDB code, both the PDB...

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Autores principales: Lübben, Anna V., Sheldrick, George M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6557183/
https://www.ncbi.nlm.nih.gov/pubmed/31236096
http://dx.doi.org/10.1107/S1600576719005478
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author Lübben, Anna V.
Sheldrick, George M.
author_facet Lübben, Anna V.
Sheldrick, George M.
author_sort Lübben, Anna V.
collection PubMed
description The open-source Python program PDB2INS is designed to prepare a .ins file for refinement with SHELXL [Sheldrick (2015). Acta Cryst. C71, 3–8], taking atom coordinates and other information from a Protein Data Bank (PDB)-format file. If PDB2INS is provided with a four-character PDB code, both the PDB file and the accompanying mmCIF-format reflection data file (if available) are accessed via the internet from the PDB public archive [Read et al. (2011). Structure, 19, 1395–1412] or optionally from the PDB_REDO server [Joosten, Long, Murshudov & Perrakis (2014). IUCrJ, 1, 213–220]. The SHELX-format .ins (refinement instructions and atomic coordinates) and .hkl (reflection data) files can then be generated without further user intervention, appropriate restraints etc. being added automatically. PDB2INS was tested on the 23 974 X-ray structures deposited in the PDB between 2008 and 2018 that included reflection data to 1.7 Å or better resolution in a recognizable format. After creating the two input files for SHELXL without user intervention, ten cycles of conjugate-gradient least-squares refinement were performed. For 96% of these structures PDB2INS and SHELXL completed successfully without error messages.
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spelling pubmed-65571832019-06-24 PDB2INS: bridging the gap between small-molecule and macromolecular refinement Lübben, Anna V. Sheldrick, George M. J Appl Crystallogr Computer Programs The open-source Python program PDB2INS is designed to prepare a .ins file for refinement with SHELXL [Sheldrick (2015). Acta Cryst. C71, 3–8], taking atom coordinates and other information from a Protein Data Bank (PDB)-format file. If PDB2INS is provided with a four-character PDB code, both the PDB file and the accompanying mmCIF-format reflection data file (if available) are accessed via the internet from the PDB public archive [Read et al. (2011). Structure, 19, 1395–1412] or optionally from the PDB_REDO server [Joosten, Long, Murshudov & Perrakis (2014). IUCrJ, 1, 213–220]. The SHELX-format .ins (refinement instructions and atomic coordinates) and .hkl (reflection data) files can then be generated without further user intervention, appropriate restraints etc. being added automatically. PDB2INS was tested on the 23 974 X-ray structures deposited in the PDB between 2008 and 2018 that included reflection data to 1.7 Å or better resolution in a recognizable format. After creating the two input files for SHELXL without user intervention, ten cycles of conjugate-gradient least-squares refinement were performed. For 96% of these structures PDB2INS and SHELXL completed successfully without error messages. International Union of Crystallography 2019-05-14 /pmc/articles/PMC6557183/ /pubmed/31236096 http://dx.doi.org/10.1107/S1600576719005478 Text en © Lübben & Sheldrick 2019 http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/4.0/
spellingShingle Computer Programs
Lübben, Anna V.
Sheldrick, George M.
PDB2INS: bridging the gap between small-molecule and macromolecular refinement
title PDB2INS: bridging the gap between small-molecule and macromolecular refinement
title_full PDB2INS: bridging the gap between small-molecule and macromolecular refinement
title_fullStr PDB2INS: bridging the gap between small-molecule and macromolecular refinement
title_full_unstemmed PDB2INS: bridging the gap between small-molecule and macromolecular refinement
title_short PDB2INS: bridging the gap between small-molecule and macromolecular refinement
title_sort pdb2ins: bridging the gap between small-molecule and macromolecular refinement
topic Computer Programs
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6557183/
https://www.ncbi.nlm.nih.gov/pubmed/31236096
http://dx.doi.org/10.1107/S1600576719005478
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