Developments in the CCP4 molecular-graphics project.

By Liz Potterton, S. McNicholas, Eugene Krissinel, Jan Gruber, Kevin Cowtan, P. Emsley, G. Murshudov, Serge X. Cohen, Anastassis Perrakis, Martin Noble. 2004

582 citations recorded by the source corpus.

Progress towards structure determination that is both high-throughput and high-value is dependent on the development of integrated and automatic tools for electron-density map interpretation and for the analysis of the resulting atomic models. Advances in map-interpretation algorithms are extending the resolution regime in which fully automatic tools can work reliably, but at present human intervention is required to interpret poor regions of macromolecular electron density, particularly where crystallographic data is only available to modest resolution [for example, I/sigma(I) < 2.0 for minimum resolution 2.5 A]. In such cases, a set of manual and semi-manual model-building molecular-graphics tools is needed. At the same time, converting the knowledge encapsulated in a molecular structure into understanding is dependent upon visualization tools, which must be able to communicate that understanding to others by means of both static and dynamic representations. CCP4 mg is a program designed to meet these needs in a way that is closely integrated with the ongoing development of CCP4 as a program suite suitable for both low- and high-intervention computational structural biology. As well as providing a carefully designed user interface to advanced algorithms of model building and analysis, CCP4 mg is intended to present a graphical toolkit to developers of novel algorithms in these fields.

Subfields: Materials Chemistry, Molecular Biology, Computational Biology & Bioinformatics

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Citations in the corpus

Using SAD data in Phaser (2011, positive): “Read & McCoy Using SAD data in Phaser 341 Figure 4 Log-likelihood gradient (LLG) maps, contoured at +6 (cyan contours) and À6 (magenta contours) times the r.m.s. deviation of the LLG map; this figure was prepared using CCP4mg (Potterton et al., 2004).”
Features and development of Coot (2010, neutral): “Coot can write CCP 4 mg picture-deﬁnition ﬁles (Potterton et al. , 2004).”
Overview of the CCP4 suite and current developments (2011, methodology): “As well as displaying coordinates in a wide variety of styles, CCP4mg can display molecular surfaces, electron density, arbitrary vectors and labels.”
Phaser crystallographic software (2007, methodology): “At about the same time, Python was chosen as a scripting language by PHENIX, ccp4mg (Potterton et al., 2002, 2004) and PyMol (DeLano, 2002), amongst others.”
Crystal Structure of the Bacterial Luciferase/Flavin Complex Provides Insight into the Function of the β Subunit (2009, unknown): “Subsequent analysis and refinement was carried out with a combination of CCP4i, andCoot (23-25).”
Crystal structure of the TLR4-MD-2 complex with bound endotoxin antagonist Eritoran. (2007, unknown): “The surface potential was calculated and displayed using the CCP4 mg program (Potterton et al., 2004).”
Presenting your structures: the CCP4mg molecular-graphics software (2011, methodology): “CCP4mg has been developed as an easy-to-use yet flexible system for displaying the structure and structure-based properties of macromolecules (Potterton et al., 2002, 2004).”
The Structure, Stability and Pheromone Binding of the Male Mouse Protein Sex Pheromone Darcin (2014, background): “Surface analysis used NACCESS (Hubbard,S.J. & Thornton, J.M. (1993), ‘NACCESS’, Computer Program, Department of Biochemistry and Molecular Biology, University College London) for identification of exposed hydrophobic residues, CCP4MG [41] for calculation and displaying electrostatic surface potentia”
JLigand: a graphical tool for the CCP4 template-restraint library (2012, methodology): “The library is also used in Coot (Emsley et al., 2010) for input of data required for real-space refinement of ligands and in CCP4mg (Potterton et al., 2004).”