Graphical tools for macromolecular crystallography in PHENIX
By Nathaniel Echols, R. Grosse-Kunstleve, Pavel V. Afonine, G. Bunkoczi, Vincent B. Chen, J. Headd, A. McCoy, Nigel W. Moriarty, Randy J. Read, David C Richardson and 3 more. 2012
153 citations recorded by the source corpus.
The foundations and current features of a widely used graphical user interface for macromolecular crystallography are described.
Subfields: Materials Chemistry, Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- Paul D. Adams
- Pavel V. Afonine
- T. C. Terwilliger
- Randy J. Read
- Nigel W. Moriarty
- Nathaniel Echols
- A. McCoy
- G. Bunkoczi
In Molecular Biology
- Paul D. Adams
- Pavel V. Afonine
- T. C. Terwilliger
- Randy J. Read
- Nathaniel Echols
- Nigel W. Moriarty
- A. McCoy
- Jane S. Richardson
Citations in the corpus
- An editor for the generation and customization of geometry restraints (2017, unknown): “REEL can be started on the command line as a standalone GUI, but is also available in the main PHENIX GUI as a choice in the Ligands menu, as well as being integrated into other program results pages.”
- RNA Structure Refinement using the ERRASER-Phenix pipeline (2013, methodology): “The validation display is identical to the all-atom contact and RNA-specific components in the Phenix GUI, which interact directly with Coot (20).”
- Interactive comparison and remediation of collections of macromolecular structures (2018, background): “31 After the initial calculations are complete, all models and maps are loaded into one or both viewers.”
- Model morphing and sequence assignment after molecular replacement (2013, methodology): “…can carry out morphing and sequence assignment and instructions for their use are available as part of the Phenix GUI (http://www.phenix-online.org; Echols et al., 2012), which is freely available to academic users both as binaries for standard Macintosh, Windows and Linux platforms, and as source…”
- Computational Methods for RNA Structure Validation and Improvement. (2015, methodology): “As a crystallographer, the most helpful form of validation and correction is to work within the PHENIX GUI (Echols et al., 2012), where MolProbity-style validation is reported at the end of each macrocycle in tables, plots, and a multi-criterion kinemage.”
- Phaser.MRage: automated molecular replacement (2013, methodology): “A tutorial introduction (explaining input preparation through the GUI, but also showing the resulting command script) is available at http://www.phaser.cimr.cam.ac.uk/index.php/ Molecular_replacement_with_MRage.”