Recent developments in classical density modification

By Kevin Cowtan. 2010

424 citations recorded by the source corpus.

Several new methods are evaluated for use in the improvement of experimental phases in the framework of a classical density-modification calculation. These methods have been implemented in a new computer program, Parrot.

Subfields: Atomic and Molecular Physics, and Optics, Structural Biology, Surfaces, Coatings and Films

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Atomic and Molecular Physics, and Optics

1. Paul D. Adams
2. T. C. Terwilliger
3. Li-Wei Hung
4. G. Bunkoczi
5. Petrus H. Zwart
6. Janet L. Smith
7. D. Akey
8. S. W. Hoh

In Structural Biology

1. S. W. Hoh
2. Tom Burnley
3. T. C. Terwilliger
4. Kevin Cowtan
5. Paul D. Adams
6. Li-Wei Hung
7. G. Bunkoczi
8. Petrus H. Zwart

In Surfaces, Coatings and Films

1. S. W. Hoh
2. Tom Burnley
3. Kevin Cowtan
4. T. C. Terwilliger
5. Paul D. Adams
6. Li-Wei Hung
7. G. Bunkoczi
8. Petrus H. Zwart

Citations in the corpus

• Features and development of Coot (2010, neutral): “Currently, suitable files are generated by the following software: Phaser (Storoni et al. , 2004), REFMAC (Murshudov et al. , 1997), phenix.refine (Adams et al. , 2002), DM (Zhang et al. , 1997), Parrot (Cowtan, 2010), Pirate (Cowtan, 2000) and BUSTER (Blanc et al. , 2004).”
• Overview of the CCP4 suite and current developments (2011, positive): “The latest program Parrot (Cowtan, 2010) achieves similar improvements but is also fast and automated.”
• Structure of Respiratory Syncytial Virus Fusion Glycoprotein in the Postfusion Conformation Reveals Preservation of Neutralizing Epitopes (2011, background): “The asymmetric unit contained two six-helix bundles, and the phases were greatly improved by 6-fold noncrystallographic symmetry aver- aging using PARROT, with the figure of merit improving from 0.181 to 0.677 (15).”
• Ab initio solution of macromolecular crystal structures without direct methods (2017, background): “At this point, the phase information was sufficient to enable phase improvement by density modification in Parrot (18), and the resulting map could be interpreted in terms of an atomic model in ARP/wARP (19).”
• FEM: feature-enhanced map (2014, neutral): “(iv) Density-modification techniques (for reviews, see Podjarny et al., 1996; Zhang et al., 2006; Cowtan, 2010).”
• Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM (2020, methodology): “Densitymodification, iterative model-building and refinement procedures are then performed to improve the initial maps and phases (Cowtan & Zhang, 1999; Terwilliger, 2000, 2002; Terwilliger et al., 2008; Cowtan, 2010).”
• Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing (2016, methodology): “…map is normally then improved by density-modification techniques (Wang, 1985; Cowtan & Main, 1996; Abrahams & Leslie, 1996; Terwilliger, 2000; Cowtan, 2010) and interpreted in terms of an atomic model (see, for example, Jones et al., 1991; Perrakis et al., 1999; Emsley et al., 2010;…”