Jmol – a paradigm shift in crystallographic visualization

By Robert M. Hanson. 2010

306 citations recorded by the source corpus.

Subfields: Molecular Biology, Organic Chemistry, Physical and Theoretical Chemistry

How researchers see this paper

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

In Molecular Biology

1. Paul D. Adams
2. Pavel V. Afonine
3. Nigel W. Moriarty
4. O. Sobolev
5. G. Murshudov
6. D. Liebschner
7. Billy K. Poon
8. Martin Noble

In Organic Chemistry

1. Jose M. Duarte
2. Nicholas B Rego
3. Paul D. Adams
4. David Ryan Koes
5. Yana Valasatava
6. Pavel V. Afonine
7. Nigel W. Moriarty
8. Peter W. Rose

In Physical and Theoretical Chemistry

1. Alexander S. Rose
2. Pavel V. Afonine
3. Jose M. Duarte
4. Rajarshi Guha
5. Nicholas B Rego
6. Paul D. Adams
7. David Ryan Koes
8. Christoph Steinbeck

Citations in the corpus

• 3Dmol.js: molecular visualization with WebGL (2014, background): “An alternative to the software-based rendering of Jmol/JSmol is to use hardware-accelerated graphics, as is done with desktop applications.”
• BioJava: an open-source framework for bioinformatics in 2012 (2012, methodology): “For visualization, an interface to the 3D viewer Jmol (Hanson, 2010) http://www.jmol.org/ is provided.”
• Memoir: template-based structure prediction for membrane proteins (2013, unknown): “These are displayed in the Jmol 3D graphics viewer (17) and are available for download in PDB format (Figure 2a).”
• The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching (2017, background): “Originally, the CDK was developed as a shared library between JChemPaint [76] and Jmol [77, 78].”
• NGL viewer: web‐based molecular graphics for large complexes (2018, methodology): “These include, JSmol, the Jmol port to JavaScript/HTML 5 (Hanson, 2010) and the WebGL-based viewers 3Dmol.js (Rego and Koes, 2015), ChemDoodle (Burger, 2015), iCn3D github.com/ncbi/icn3d, PV github.com/biasmv/pv, LiteMol (Sehnal et al., 2017), Molmil (Bekker et al., 2016), NGL Viewer (Rose and…”
• Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). (2019, methodology): “…software applications, including CCP4mg (Potterton et al., 2004), Coot (Brown et al., 2015), Chimera (Goddard et al., 2018), Jmol/JSMol (Hanson, 2010; Hanson et al., 2013), LiteMole (Sehnal et al., 2017), Molmil (Bekker et al., 2016), NGL (Rose et al., 2018), 452 Paul D. Adams et al.…”