iotbx.cif: a comprehensive CIF toolbox.

doi:10.1107/S0021889811041161

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iotbx.cif: a comprehensive CIF toolbox.

Journal Article•DOI•

iotbx.cif: a comprehensive CIF toolbox.

Richard J. Gildea¹, Richard J. Gildea², Luc J. Bourhis², Oleg V. Dolomanov², Ralf W. Grosse-Kunstleve¹, Horst Puschmann², Paul D. Adams¹, Judith A. K. Howard² - Show less +4 more•Institutions (2)

Lawrence Berkeley National Laboratory¹, Durham University²

01 Dec 2011-Journal of Applied Crystallography (International Union of Crystallography)-Vol. 44, Iss: 6, pp 1259-1263

TL;DR: CIF.iotbx.cif is a comprehensive toolbox for the development of applications that make use of the CIF format.

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Abstract: iotbx.cif is a new software module for the development of applications that make use of the CIF format. Comprehensive tools are provided for input, output and validation of CIFs, as well as for interconversion with high-level cctbx [Grosse-Kunstleve, Sauter, Moriarty & Adams (2002). J. Appl. Cryst. 35, 126–136] crystallographic objects. The interface to the library is written in Python, whilst parsing is carried out using a compiled parser, combining the performance of a compiled language (C++) with the benefits of using an interpreted language.

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Journal Article•DOI•

J. Appl. Cryst.の発刊に際して

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良二上田

10 Mar 1970

8,159 citations

Journal Article•DOI•

The anatomy of a comprehensive constrained, restrained refinement program for the modern computing environment – Olex2 dissected

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Luc J. Bourhis¹, Oleg V. Dolomanov², Richard J. Gildea, Judith A. K. Howard², Horst Puschmann² - Show less +1 more•Institutions (2)

Bruker¹, Durham University²

01 Jan 2015-Acta Crystallographica Section A

TL;DR: An in-depth presentation is given of olex2.refine, the new refinement engine integrated in the Olex2 program.

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Abstract: This paper describes the mathematical basis for olex2.refine, the new refinement engine which is integrated within the Olex2 program. Precise and clear equations are provided for every computation performed by this engine, including structure factors and their derivatives, constraints, restraints and twinning; a general overview is also given of the different components of the engine and their relation to each other. A framework for adding multiple general constraints with dependencies on common physical parameters is described. Several new restraints on atomic displacement parameters are also presented.

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1,012 citations

Cites methods from "iotbx.cif: a comprehensive CIF tool..."

...As part of this work a CIF-handling toolbox (Gildea et al., 2011) was added to cctbx....
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Journal Article•DOI•

Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins *

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Chao Xu¹, Ke Liu¹, Hazem Ahmed¹, Peter Loppnau¹, Matthieu Schapira¹, Jinrong Min¹, Jinrong Min² - Show less +3 more•Institutions (2)

Structural Genomics Consortium¹, University of Toronto²

09 Oct 2015-Journal of Biological Chemistry

TL;DR: The binding characteristics of the human YTH domain proteins, as well as yeast Pho92, are investigated, and the discriminative recognition of m6A among different YTH domains is indicated and only YTHDC1 harbors a distinctly selective binding pocket for the nucleotide preceding the m 6A nucleotide.

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208 citations

Cites methods from "iotbx.cif: a comprehensive CIF tool..."

...PDB deposition data were compiled with PDB_EXTRACT (36), and summarizing statistics were extracted with the IOTBX (37) software library....
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Journal Article•DOI•

COD::CIF::Parser: an error‐correcting CIF parser for the Perl language

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Andrius Merkys¹, Antanas Vaitkus¹, Justas Butkus, Mykolas Okulič-Kazarinas¹, Visvaldas Kairys¹, Saulius Gražulis¹ - Show less +2 more•Institutions (1)

Vilnius University¹

01 Feb 2016-Journal of Applied Crystallography

TL;DR: A syntax-correcting CIF parser, COD::CIF::Parser, is described that can parse CIF 1.1 files and accurately report the position and nature of the discovered syntactic problems while automatically correcting the most common and the most obvious syntactic deficiencies.

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Abstract: A syntax-correcting CIF parser, COD::CIF::Parser, is presented that can parse CIF 1.1 files and accurately report the position and the nature of the discovered syntactic problems. In addition, the parser is able to automatically fix the most common and the most obvious syntactic deficiencies of the input files. Bindings for Perl, C and Python programming environments are available. Based on COD::CIF::Parser, the cod-tools package for manipulating the CIFs in the Crystallography Open Database (COD) has been developed. The cod-tools package has been successfully used for continuous updates of the data in the automated COD data deposition pipeline, and to check the validity of COD data against the IUCr data validation guidelines. The performance, capabilities and applications of different parsers are compared.

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146 citations

Cites background from "iotbx.cif: a comprehensive CIF tool..."

...…McMahon, 2006b) and vcif2 (also known by the name of the executable file cif2cbf ; Todorov & Bernstein, 2008) in C, ucif (Gildea et al., 2011) in C++, cif2cif (Hall & Bernstein, 1996) in Fortran and PyCIFRW (Hester, 2006) in Python (van Rossum, 2003)....
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Journal Article•DOI•

Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation.

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Chao Xu¹, Ke Liu², Wolfram Tempel¹, Marina Demetriades³, Wei Shen Aik³, Christopher J. Schofield³, Jinrong Min² - Show less +3 more•Institutions (3)

Structural Genomics Consortium¹, Central China Normal University², University of Oxford³

20 Jun 2014-Journal of Biological Chemistry

TL;DR: Insight is provided into the molecular mechanism of ALKBH5 as an m6A ssRNA demethylase and the design of selective inhibitors and the structural basis of its substrate selectivity and inhibition by citrate is revealed.

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134 citations

Cites methods from "iotbx.cif: a comprehensive CIF tool..."

...The data were compiled using PDB_EXTRACT (57), PHENIX (58), and IOTBX (59) software....
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Journal Article•DOI•

A short history of SHELX

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George M. Sheldrick¹•Institutions (1)

University of Göttingen¹

01 Jan 2008-Acta Crystallographica Section A

TL;DR: This paper could serve as a general literature citation when one or more of the open-source SH ELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.

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Abstract: An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.

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81,116 citations

"iotbx.cif: a comprehensive CIF tool..." refers methods in this paper

...Whilst there existed several partial CIF parsers within the cctbx, each hand-crafted to suit a specific task [separate tools for reading the PDB chemical components and CCP4 monomer libraries (Painter & Merritt, 2004); as part of the phenix.cif_as_mtz tool; for reading fcf reflection files as output by SHELXL (Sheldrick, 2008)], a comprehensive CIF parser that was tightly integrated with the rest of the library was conspicuously absent....
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...…PDB chemical components and CCP4 monomer libraries (Painter & Merritt, 2004); as part of the phenix.cif_as_mtz tool; for reading fcf reflection files as output by SHELXL (Sheldrick, 2008)], a comprehensive CIF parser that was tightly integrated with the rest of the library was conspicuously absent....
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Journal Article•DOI•

OLEX2: a complete structure solution, refinement and analysis program

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Oleg V. Dolomanov¹, Luc J. Bourhis¹, Richard J. Gildea¹, Judith A. K. Howard¹, Horst Puschmann¹ - Show less +1 more•Institutions (1)

Durham University¹

01 Apr 2009-Journal of Applied Crystallography

TL;DR: OLEX2 seamlessly links all aspects of the structure solution, refinement and publication process and presents them in a single workflow-driven package, with the ultimate goal of producing an application which will be useful to both chemists and crystallographers.

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Abstract: New software, OLEX2, has been developed for the determination, visualization and analysis of molecular crystal structures. The software has a portable mouse-driven workflow-oriented and fully comprehensive graphical user interface for structure solution, refinement and report generation, as well as novel tools for structure analysis. OLEX2 seamlessly links all aspects of the structure solution, refinement and publication process and presents them in a single workflow-driven package, with the ultimate goal of producing an application which will be useful to both chemists and crystallographers.

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19,990 citations

"iotbx.cif: a comprehensive CIF tool..." refers background or methods in this paper

...The iotbx.cif module is now used heavily by the OLEX2 (Dolomanov et al., 2009) and PHENIX (Adams et al., 2010) software packages....
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...During the development of the smtbx (small-molecule toolbox) and OLEX2 (Dolomanov et al., 2009), it became apparent that the CIF format would play a central part in presenting the results of the procedures developed....
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...In addition, there was a need to provide an interface for managing the contents of the CIF within OLEX2....
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Journal Article•DOI•

PHENIX: a comprehensive Python-based system for macromolecular structure solution

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Paul D. Adams¹, Paul D. Adams², Pavel V. Afonine², Gábor Bunkóczi³, Vincent B. Chen⁴, Ian W. Davis⁴, Nathaniel Echols², Jeffrey J. Headd⁴, Li-Wei Hung⁵, Gary J. Kapral⁴, Ralf W. Grosse-Kunstleve², Airlie J. McCoy³, Nigel W. Moriarty², Robert D. Oeffner³, Randy J. Read³, David S. Richardson⁴, Jane S. Richardson⁴, Thomas C. Terwilliger⁵, Peter H. Zwart² - Show less +15 more•Institutions (5)

University of California, Berkeley¹, Lawrence Berkeley National Laboratory², University of Cambridge³, Duke University⁴, Los Alamos National Laboratory⁵

01 Feb 2010-Acta Crystallographica Section D-biological Crystallography

TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.

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Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.

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18,531 citations

"iotbx.cif: a comprehensive CIF tool..." refers methods in this paper

...The iotbx.cif module is now used heavily by the OLEX2 (Dolomanov et al., 2009) and PHENIX (Adams et al., 2010) software packages....
[...]

Journal Article•DOI•

Structure validation in chemical crystallography

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Anthony L. Spek¹•Institutions (1)

Utrecht University¹

01 Feb 2009-Acta Crystallographica Section D-biological Crystallography

TL;DR: This paper reports on the current status of structure validation in chemical crystallography and describes the current state of research in this area.

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Abstract: Automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions.

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13,163 citations

"iotbx.cif: a comprehensive CIF tool..." refers background in this paper

...The CIF (Crystallographic Information File) syntax (Hall et al., 1991) has become firmly established (Brown & McMahon, 2002; Spek, 2009) as the file format for deposition and archiving of small-molecule crystal structures and increasingly their structure factors....
[...]

Journal Article•DOI•

J. Appl. Cryst.の発刊に際して

[...]

良二上田

10 Mar 1970

8,159 citations

"iotbx.cif: a comprehensive CIF tool..." refers background or methods in this paper

...Several CIF programming libraries have been developed for various languages and environments, including Fortran (Hall & Bernstein, 1996; Rodriguez-Carvajal & González-Platas, 2003), C (Ellis & Bernstein, 2001; Westbrook et al., 1997), Objective C (Chang & Bourne, 1998), ....
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...The interface to the library is written in Python, whilst parsing is carried out using a compiled parser, combining the performance of a compiled language (C++) with the benefits of using an interpreted language....
[...]