List of molecular graphics systems

This is a list of notable software systems that are used for visualizing macromolecules.^[1]

Name	Data	License	Technology	Citations	Comments
Amira	EM MM MRI Optical SMI XRD	Proprietary^[2]	Windows, Linux, Mac	^[3]^{[self-published source?]}	Based on OpenInventor/OpenGL; focusing on life and biomedical sciences.
Ascalaph Designer	MM MD QM	Proprietary	C++	^[4]^{[self-published source?]}	Graphics, model building, molecular mechanics, quantum chemistry.
Avizo	EM MM MRI Optical SMI XRD	Proprietary^[5]	Windows, Linux, Mac	^[6]^{[self-published source?]}	Avizo is derived from Amira and focusing on materials science.
Avogadro	MM XRD MD	Free open-source, GPL	C++, Qt, extensible via Python modules
BALL	Molecular dynamics MM NMR	LGPL open-source	Standalone program	^[7]
Cn3D		Free open-source	Standalone program	^[8]	In the NCBI C++ toolkit
Coot	XRD	Free open-source
Gabedit	XRD MM	Free open-source	C	^[9]
Jmol		Free open-source	Java (applet or standalone program) Transpiled HTML5/JavaScript for browser	^[10]^{[self-published source?]}	Supports advanced capabilities such as loading multiple molecules with independent movement, surfaces and molecular orbitals, cavity visualization, crystal symmetry
MDL Chime		Proprietary, free use noncommercial	C++ browser plugin for Windows only	^[11]^{[self-published source?]}	Build and visualize molecule and periodic systems (crystal, structures, fluids...), animate trajectories, visualize molecular orbitals, density, electrostatic potential... visualize graph such IR, NMR, dielectric and optical tensors.
Molden	MM XRD	Proprietary, free use academic		^[12]
Molecular Operating Environment (MOE)	HM MD MM NA QM SMI XRD	Proprietary	Windows, Linux, OS X; SVL programming language		Build, edit and visualise small molecules, macromolecules, protein-ligand complexes, crystal lattices, molecular and property surfaces. Platform for extensive collection of molecular modelling / drug discovery applications.
Molekel	MM XRD	Free open-source	Java 3D applet or standalone program
Ovito	MM XRD EM MD	Free open-source	Python	^[13] ^[14]
PyMOL	MM XRD SMI EM	Open-source^[15]	Python	^[16]^{[self-published source?]}	According to the author, almost 1/4 of all published images of 3D protein structures in the scientific literature were made via PyMOL.^{[citation needed]}
RasMol		Free open-source	C standalone program	^[17]^[18]^[19]^{[self-published source?]}
SAMSON	MM MD SMI MRI	Proprietary, limited free version	Windows, Linux, Mac. C++ (Qt)	^[20]	Computational nanoscience: life sciences, materials, etc. Modular architecture, modules termed SAMSON Elements.
Sirius		Free open-source	Java 3D applet or standalone program		No longer supported as of 2011.
Scigress	MM QM	Proprietary^[21]	Standalone program	^[22]	Edit, visualize and run simulations on various molecular systems.
Spartan	MM QM	Proprietary^[23]	Standalone program	^[24]	Visualize and edit biomolecules, extract bound ligands from PDB files for further computational analysis, full molecular mechanics and quantum chemical calculations package with streamlined graphical user interface.
UCSF Chimera	XRD SMI EM MD	Free open-source^[25] for noncommercial use^[26]	Python	^[27]^[28]^{[self-published source?]}	Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.^[29]
VMD	EM MD MM	Free open-source for noncommercial use^[30]	C++	^[31]^[32]^{[self-published source?]}
WHAT IF	HM XRD	Proprietary, shareware for academics	Fortran, C, OpenGL, standalone	^[33]^{[self-published source?]}	Old-fashioned interface; very good software for the experienced bioinformatician; nearly 2000 protein-structure related options; comes with 500 page writeup.
YASARA	HM NMR XRC	Proprietary, limited free version	C-assembly, Windows, Linux, Mac	^[34]^{[self-published source?]}	Fully featured molecular modeling and simulation program, incl., structure prediction and docking. Graphical or text mode (clusters), Python interface.

Key

The tables below indicate which types of data can be visualized in each system:

EM – Electron microscopy
HM – Homology modeling
MD – Molecular dynamics
MM – Molecular modelling, molecular orbital visualizing
MRI – Magnetic resonance imaging
NA – Nucleic acids
NMR – Nuclear magnetic resonance
Optical – Optical microscopy
QM – Quantum chemistry
SMI – Small molecule interactions
XRD – X-ray crystallography data such as electron density

References

^ O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, et al. (March 2010). "Visualization of macromolecular structures". Nature Methods. 7 (3 Suppl): S42-55. doi:10.1038/nmeth.1427. PMC 7097155. PMID 20195256.
^ Amira commercial license
^ "Amira for Life & Biomedical Sciences". 2019-02-28. Retrieved February 28, 2019.
^ "Ascalaph". Retrieved 24 September 2009.
^ Avizo commercial license
^ "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data". 2018-09-26. Retrieved August 5, 2010.
^ Hildebrandt, Andreas (25 October 2010). "BALL - biochemical algorithms library 1.3". BMC Bioinformatics. 11: 531. doi:10.1186/1471-2105-11-531. PMC 2984589. PMID 20973958.
^ Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH (June 2000). "Cn3D: sequence and structure views for Entrez". Trends in Biochemical Sciences. 25 (6): 300–2. doi:10.1016/S0968-0004(00)01561-9. PMID 10838572.
^ "Gabedit A graphical user interface for computational chemistry packages".
^ "Jmol: an open-source Java viewer for chemical structures in 3D". Retrieved 24 September 2009.
^ "Chime Pro". Symx. Retrieved 24 September 2009.
^ "Molden a visualization program of molecular and electronic structure".
^ {{cite web |url=http://doi.org/10.1088/0965-0393/18/1/015012 |title=Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool
^ {{cite web |url=https://gitlab.com/stuko/ovito/-/blob/master/LICENSE.txt |title=OVITO License | website = GitLab | access-date=2024-10-218
^ "PyMOL License". GitHub. Jan 8, 2010. Retrieved 2023-03-27.
^ "PyMOL Molecular Viewer". Retrieved 24 September 2009.
^ Sayle RA, Milner-White EJ (September 1995). "RASMOL: biomolecular graphics for all". Trends in Biochemical Sciences. 20 (9): 374–376. doi:10.1016/S0968-0004(00)89080-5. PMID 7482707.
^ Bernstein HJ (September 2000). "Recent changes to RasMol, recombining the variants". Trends in Biochemical Sciences. 25 (9): 453–5. doi:10.1016/S0968-0004(00)01606-6. PMID 10973060.
^ "Home Page for RasMol and OpenRasMol". Retrieved 24 September 2009.
^ SAMSON Connect
^ Scigress commercial license
^ "Scigress". fqs.pl. 12 September 2014.
^ Spartan webpage
^ Spartan Tutorial & User's Guide ISBN 1-890661-38-4
^ "UCSF Chimera code repository". www.rbvi.ucsf.edu. Retrieved 2023-03-27.
^ UCSF Chimera license
^ Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (October 2004). "UCSF Chimera--a visualization system for exploratory research and analysis". Journal of Computational Chemistry. 25 (13): 1605–12. CiteSeerX 10.1.1.456.9442. doi:10.1002/jcc.20084. PMID 15264254. S2CID 8747218.
^ "UCSF Chimera". Retrieved 24 September 2009.
^ Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE (July 2006). "Tools for integrated sequence-structure analysis with UCSF Chimera". BMC Bioinformatics. 7: 339. doi:10.1186/1471-2105-7-339. PMC 1570152. PMID 16836757.
^ Visual Molecular Dynamics license
^ Humphrey W, Dalke A, Schulten K (February 1996). "VMD: visual molecular dynamics". Journal of Molecular Graphics. 14 (1): 33–8, 27–8. doi:10.1016/0263-7855(96)00018-5. PMID 8744570.
^ "VMD - Visual Molecular Dynamics". Retrieved 24 September 2009.
^ "WHAT IF homepage". Retrieved 24 September 2009.
^ "YASARA – Yet Another Scientific Artificial Reality Application". Retrieved 24 September 2009.

External links

Saric M. "Free Molecular Modelling Programs =". A rather detailed, objective, and technical assessment of about 20 tools.
"PDB list of molecular graphics tools".
"Index of Molecular Visualization Resources".
"Molecular Visualization Resources by Eric Martz".

[1] O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, et al. (March 2010). "Visualization of macromolecular structures". Nature Methods. 7 (3 Suppl): S42-55. doi:10.1038/nmeth.1427. PMC 7097155. PMID 20195256.

[2] Amira commercial license

[3] "Amira for Life & Biomedical Sciences". 2019-02-28. Retrieved February 28, 2019.

[4] "Ascalaph". Retrieved 24 September 2009.

[5] Avizo commercial license

[6] "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data". 2018-09-26. Retrieved August 5, 2010.

[7] Hildebrandt, Andreas (25 October 2010). "BALL - biochemical algorithms library 1.3". BMC Bioinformatics. 11: 531. doi:10.1186/1471-2105-11-531. PMC 2984589. PMID 20973958.

[8] Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH (June 2000). "Cn3D: sequence and structure views for Entrez". Trends in Biochemical Sciences. 25 (6): 300–2. doi:10.1016/S0968-0004(00)01561-9. PMID 10838572.

[9] "Gabedit A graphical user interface for computational chemistry packages".

[10] "Jmol: an open-source Java viewer for chemical structures in 3D". Retrieved 24 September 2009.

[11] "Chime Pro". Symx. Retrieved 24 September 2009.

[12] "Molden a visualization program of molecular and electronic structure".

[13] {{cite web |url=http://doi.org/10.1088/0965-0393/18/1/015012 |title=Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool

[14] {{cite web |url=https://gitlab.com/stuko/ovito/-/blob/master/LICENSE.txt |title=OVITO License | website = GitLab | access-date=2024-10-218

[15] "PyMOL License". GitHub. Jan 8, 2010. Retrieved 2023-03-27.

[16] "PyMOL Molecular Viewer". Retrieved 24 September 2009.

[17] Sayle RA, Milner-White EJ (September 1995). "RASMOL: biomolecular graphics for all". Trends in Biochemical Sciences. 20 (9): 374–376. doi:10.1016/S0968-0004(00)89080-5. PMID 7482707.

[18] Bernstein HJ (September 2000). "Recent changes to RasMol, recombining the variants". Trends in Biochemical Sciences. 25 (9): 453–5. doi:10.1016/S0968-0004(00)01606-6. PMID 10973060.

[19] "Home Page for RasMol and OpenRasMol". Retrieved 24 September 2009.

[20] SAMSON Connect

[21] Scigress commercial license

[22] "Scigress". fqs.pl. 12 September 2014.

[23] Spartan webpage

[24] Spartan Tutorial & User's Guide ISBN 1-890661-38-4

[25] "UCSF Chimera code repository". www.rbvi.ucsf.edu. Retrieved 2023-03-27.

[26] UCSF Chimera license

[27] Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (October 2004). "UCSF Chimera--a visualization system for exploratory research and analysis". Journal of Computational Chemistry. 25 (13): 1605–12. CiteSeerX 10.1.1.456.9442. doi:10.1002/jcc.20084. PMID 15264254. S2CID 8747218.

[28] "UCSF Chimera". Retrieved 24 September 2009.

[29] Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE (July 2006). "Tools for integrated sequence-structure analysis with UCSF Chimera". BMC Bioinformatics. 7: 339. doi:10.1186/1471-2105-7-339. PMC 1570152. PMID 16836757.

[30] Visual Molecular Dynamics license

[31] Humphrey W, Dalke A, Schulten K (February 1996). "VMD: visual molecular dynamics". Journal of Molecular Graphics. 14 (1): 33–8, 27–8. doi:10.1016/0263-7855(96)00018-5. PMID 8744570.

[32] "VMD - Visual Molecular Dynamics". Retrieved 24 September 2009.

[33] "WHAT IF homepage". Retrieved 24 September 2009.

[34] "YASARA – Yet Another Scientific Artificial Reality Application". Retrieved 24 September 2009.

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List of molecular graphics systems

Key

See also

References

External links

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