Molecular graphics

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Molecular graphics (MG) is the discipline and philosophy of studying molecules and their properties through graphical representation.[1] IUPAC limits the definition to representations on a "graphical display device".[2] Ever since Dalton's atoms and Kekulé's benzene, there has been a rich history of hand-drawn atoms and molecules, and these representations have had an important influence on modern molecular graphics.

Colour molecular graphics are often used on chemistry journal covers in an artistic manner.[3]

History[edit]

Initially the rendering was on early Cathode ray tube screens or through plotters drawing on paper. Molecular structures have always been an attractive choice for developing new computer graphics tools, since the input data are easy to create and the results are usually highly appealing. The first example of MG was a display of a protein molecule (Project MAC, 1966) by Cyrus Levinthal and Robert Langridge. Among the milestones in high-performance MG was the work of Nelson Max in "realistic" rendering of macromolecules using reflecting spheres.

Initially much of the technology concentrated on high-performance 3D graphics.[4] During the 1980s a number of programs for calculating molecular properties became available and molecular graphics often included these calculations.

The requirements of macromolecular crystallography also drove MG because the traditional techniques of physical model-building could not scale. The first two protein structures solved by molecular graphics without the aid of the Richards' Box were built with Stan Swanson's program FIT on the Vector General graphics display in the laboratory of Edgar Meyer at Texas A&M University: First Marge Legg in Al Cotton's lab at A&M solved a second, higher-resolution structure of staph. nuclease (1975) and then Jim Hogle solved the structure of monoclinic lysozyme in 1976. A full year passed before other graphics systems were used to replace the Richards' Box for modelling into density in 3-D. Alwyn Jones' FRODO program (and later "O") were developed to overlay the molecular electron density determined from X-ray crystallography and the hypothetical molecular structure.

In 2009 BALLView became the first software to use realtime Raytracing for molecular graphics.

Chronology[edit]

Developer(s) Approximate date Technology Comments
Crystallographers < 1960 Hand-drawn Crystal structures, with hidden atom and bond removal. Often clinographic projections.
Johnson, Motherwell c. 1970 Pen plotter ORTEP, PLUTO. Very widely deployed for publishing crystal structures.
Cyrus Levinthal, Bob Langridge, Ward, Stots[5] 1966 Project MAC display system, two-degree of freedom, spring-return velocity joystick for rotating the image. First protein display on screen. System for interactively building protein structures.
Barry[6] 1969 LINC 300 computer with a dual trace oscilloscope display. Interactive molecular structure viewing system. Early examples of dynamic rotation, intensity depth·cueing, and side-by-side stereo. Early use of the small angle approximations (a = sin a, 1 = cos a) to speed up graphical rotation calculations.
Ortony[7] 1971 Designed a stereo viewer (British patent appl. 13844/70) for molecular computer graphics. Horizontal two-way (half-silvered) mirror combines images drawn on the upper and lower halves of a CRT. Crossed polarizers isolate the images to each eye.
Ortony[8] 1971 Light pen, knob. Interactive molecular structure viewing system. Select bond by turning another knob until desired bond lights up in sequence, a technique later used on the MMS-4 system below, or by picking with the light pen. Points in space are specified with a 3-D ”bug" under dynamic control.
Barry, Graesser, Marshall[9] 1971 CHEMAST: LINC 300 computer driving an oscilloscope. Two-axis joystick, similar to one used later by GRIP-75 (below). Interactive molecular structure viewing system. Structures dynamically rotated using the joystick.
Tountas and Katz[10] 1971 Adage AGT/50 display Interactive molecular structure viewing system. Mathematics of nested rotation and for laboratory-space rotation.
Perkins, Piper, Tattam, White[11] 1971 Honeywell DDP 516 computer, EAL TR48 analog computer, Lanelec oscilloscope, 7 linear potentiometers. Stereo. Interactive molecular structure viewing system.
Wright[12][13][14] 1972 GRIP-71 at UNC-CH: IBM System/360 Model 40 time-shared computer, IBM 2250 display, buttons, light pen, keyboard. Discrete manipulation and energy relaxation of protein structures. Program code became the foundation of the GRIP-75 system below.
Barry and North[15] 1972 Oxford Univ.: Ferranti Argus 500 computer, Ferranti model 30 display, keyboard, track ball, one knob. Stereo. Prototype large-molecule crystallographic structure solution system. Track ball rotates a bond, knob brightens the molecule vs. electron density map.
North, Ford, Watson Early 1970s Leeds Univ.: DEC PDP·11/40 computer, Hewlett-Packard display. 16 knobs, keyboard, spring-return joystick. Stereo. Prototype large-molecule crystallographic structure solution system. Six knobs rotate and translate a small molecule.
Barry, Bosshard, Ellis, Marshall, Fritch, Jacobi 1974 MMS-4:[16][17] Washington Univ. at St. Louis, LINC 300 computer and an LDS-1 / LINC 300 display, custom display modules. Rotation joystick, knobs. Stereo. Prototype large-molecule crystallographic structure solution system. Select bond to rotate by turning another knob until desired bond lights up in sequence.
Cohen and Feldmann[18] 1974 DEC PDP-10 computer, Adage display, push buttons, keyboard, knobs Prototype large-molecule crystallographic structure solution system.
Stellman[19] 1975 Princeton: PDP-10 computer, LDS-1 display, knobs Prototype large-molecule crystallographic structure solution system. Electron density map not shown; instead an "H Factor" figure of merit is updated as the molecular structure is manipulated.
Collins, Cotton, Hazen, Meyer, Morimoto 1975 CRYSNET,[20] Texas A&M Univ. DEC PDP-11/40 computer, Vector General Series 3 display, knobs, keyboard. Stereo. Prototype large-molecule crystallographic structure solution system. Variety of viewing modes: rocking, spinning, and several stereo display modes.
Cornelius and Kraut 1976 (approx.) Univ, of Calif. at San Diego: DEC PDP-11/40 emulator (CalData 135), Evans and Sutherland Picture System display, keyboard, 6 knobs. Stereo. Prototype large-molecule crystallographic structure solution system.
(Yale Univ.) 1976 (approx.) PIGS: DEC PDP-11/70 computer, Evans and Sutherland Picture System 2 display, data tablet, knobs. Prototype large-molecule crystallographic structure solution system. The tablet was used for most interactions.
Feldmann and Porter 1976 NIH: DEC PDP—11/70 computer. Evans and Sutherland Picture System 2 display, knobs. Stereo. Interactive molecular structure viewing system. Intended to display interactively molecular data from the AMSOM – Atlas of Macromolecular Structure on Microfiche.[21]
Rosenberger et al. 1976 MMS-X:[22] Washington Univ. at St. Louis, TI 980B computer, Hewlett-Packard 1321A display, Beehive video terminal, custom display modules, pair of 3-D spring-return joysticks, knobs. Prototype (and later successful) large-molecule crystallographic structure solution system. Successor to the MMS-4 system above. The 3-D spring-return joysticks either translate and rotate the molecular structure for viewing or a molecular substructure for fitting, mode controlled by a toggle switch.
Britton, Lipscomb, Pique, Wright, Brooks 1977 GRIP-75[14][23][24][25][26] at UNC-CH: Time-shared IBM System/360 Model 75 computer, DEC PDP 11/45 computer, Vector General Series 3 display, 3-D movement box from A.M. Noll and 3-D spring return joystick for substructure manipulation, Measurement Systems nested joystick, knobs, sliders, buttons, keyboard, light pen. First large-molecule crystallographic structure solution.[27]
Jones 1978 FRODO and RING[28][29] Max Planck Inst., Germany, RING: DEC PDP-11/40 and Siemens 4004 computers, Vector General 3404 display, 6 knobs. Large-molecule crystallographic structure solution. FRODO may have run on a DEC VAX-780 as a follow-on to RING.
Diamond 1978 Bilder[30] Cambridge, England, DEC PDP-11/50 computer, Evans and Sutherland Picture System display, tablet. Large-molecule crystallographic structure solution. All input is by data tablet. Molecular structures built on-line with ideal geometry. Later passes stretch bonds with idealization.
Langridge, White, Marshall Late 1970s Departmental systems (PDP-11, Tektronix displays or DEC-VT11, e.g. MMS-X) Mixture of commodity computing with early displays.
Davies, Hubbard Mid-1980s CHEM-X, HYDRA Laboratory systems with multicolor, raster and vector devices (Sigmex, PS300).
Biosym, Tripos, Polygen Mid-1980s PS300 and lower cost dumb terminals (VT200, SIGMEX) Commercial integrated modelling and display packages.
Silicon Graphics, Sun Late 1980s IRIS GL (UNIX) workstations Commodity-priced single-user workstations with stereoscopic display.
EMBL - WHAT IF 1989, 2000 Machine independent Nearly free, multifunctional, still fully supported, many free servers based on it
Sayle, Richardson 1992, 1993 RasMol, Kinemage Platform-independent MG.
MDL (van Vliet, Maffett, Adler, Holt) 1995–1998 Chime proprietary C++ ; free browser plugin for Mac (OS9) and PCs
MolSoft 1997–present ICM-Browser proprietary; free download for Windows, Mac, and Linux.[31][32]
1998- MarvinSketch & MarvinView. MarvinSpace (2005) proprietary Java applet or stand-alone application.
Community efforts 2000–present DINO, Jmol, PyMol, Avogadro, PDB, OpenStructure Open-source Java applet or stand-alone application.
NOCH 2002–present NOC Open source code molecular structure explorer
LION Bioscience / EMBL 2004–present SRS 3D Free, open-source system based on Java3D. Integrates 3D structures with sequence and feature data (domains, SNPs, etc.).
San Diego Supercomputer Center 2006–present Sirius Free for academic/non-profit institutions
Community efforts 2009–present HTML5/JavaScript viewers (ChemDoodle Web Components, GLMol, jolecule, pv, Molmil, iCn3D, 3DMol, NGL, Speck, xtal.js, UglyMol, LiteMol, JSmol) All Open-source. Require WebGL support in the browser (except for JSmol).

Types[edit]

Ball-and-stick models[edit]

A molecule of pamidronic acid, as drawn by the Jmol program. Hydrogen is white, carbon is grey, nitrogen is blue, oxygen is red, and phosphorus is orange.

In the ball-and-stick model, atoms are drawn as small sphered connected by rods representing the chemical bonds between them.

Space-filling models[edit]

Space-filling model of formic acid. Hydrogen is white, carbon is black, and oxygen is red.

In the space-filling model, atoms are drawn as solid spheres to suggest the space they occupy, in proportion to their van der Waals radii. Atome that share a bond overlap with each other.

Surfaces[edit]

A water molecule drawn with a shaded electrostatic potential isosurface. The areas highlighted in red have a net positive charge density, and the blue areas have a negative charge.

In some models, the surface of the molecule is approximated and shaded to represent a physical property of the molecule, such as electronic cherge density.

Ribbon diagrams[edit]

Image of hemagglutinin with alpha helices depicted as cylinders and the rest of the polypeptide as silver coils. The individual atoms of the polypeptide have been hidden. All of the non-hydrogen atoms in the two ligands are shown near the top of the diagram.

Ribbon diagrams are schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon shows the overall path and organization of the protein backbone in 3D, and serves as a visual framework on which to hang details of the full atomic structure, such as the balls for the oxygen atoms bound to the active site of myoglobin in the adjacent image. Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone. α-helices are shown as coiled ribbons or thick tubes, β-strands as arrows, and non-repetitive coils or loops as lines or thin tubes. The direction of the polypeptide chain is shown locally by the arrows, and may be indicated overall by a colour ramp along the length of the ribbon.[33]

See also[edit]

References[edit]

  1. ^ Dickerson, R.E.; Geis, I. (1969). The structure and action of proteins. Menlo Park, CA: W.A. Benjamin.
  2. ^ IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (1997) "molecular graphics". doi:10.1351/goldbook.MT06970
  3. ^ Harrison, Karl; Bowen, Jonathan P.; Bowen, Alice M. (2013). Ng, Kia; Bowen, Jonathan P.; McDaid, Sarah (eds.). "Electronic Visualisation in Chemistry: From Alchemy to Art". EVA London 2013 Conference Proceedings. Electronic Workshops in Computing. British Computer Society. pp. 267–274.
  4. ^ Porter TK (August 1978). "Spherical shading". ACM SIGGRAPH Computer Graphics. 12 (3): 282–5. doi:10.1145/965139.639789.
  5. ^ Levinthal, C. (June 1966). "Molecular Model-building by Computer". Scientific American. 214 (6): 42–52. Bibcode:1966SciAm.214f..42L. doi:10.1038/scientificamerican0666-42. PMID 5930597.
  6. ^ Barry, C. D., Ellis, R. A., Graesser, S. M., and Marshall, G. R. 1969. Display and Manipulation in Three Dimensions. Pertinent Comcepts in Computer Graphics, Univ. of Ill. Press, 104-153.
  7. ^ Ortony, A. (May 1971). "A System for Stereo Viewing". The Computer Journal. 14 (2): 140–4. doi:10.1093/comjnl/14.2.140. Also appears in: Conference on Displays, Institution of Electrical Engineers Conf. Pub. No. 80 (7–10 September 1971), C. Baldwin Ltd., 225-232.
  8. ^ Ortony, A. 1971b. Interactive Stereographics Conference on Displays, Institution of Electrical Engineers Conf. Pub. No. 80 (7–10 September), C. Baldwin Ltd., 185-193.
  9. ^ Barry, C. D., Ellis, R. A., Graesser, S. M., and Marshall, G. R. 1971. CHEMAST: A Computer Program for Modeling Molecular Structures. Proc. 1971 IFIP, 1552-1558.
  10. ^ Tountas, C. and Katz, L. 1971. Interactive Graphics in Molecular Biology. Real·time Three-dimensional Rotations of Images and Image Fragments. Proc. Summer Computer Simulation Conf., 1, 241-247.
  11. ^ Perkins, W.J.; Piper, E.A.; Tattam, F.G.; White, J.C. (June 1971). "Interactive stereoscopic computer displays for biomedical research". Computers and Biomedical Research. 4 (3): 249–261. doi:10.1016/0010-4809(71)90030-9. PMID 5562569.
  12. ^ Wright, W. V. 1972a. An Interactive Computer Graphic System for Molecular Studies. PhD Dissertation, University of North Carolina, Chapel Hill, North Carolina.
  13. ^ Wright, W.V. (October 1972). "The two-dimensional interface of an interactive system for molecular studies". ACM SIGPLAN Notices. 7 (10): 76–85. doi:10.1145/942576.807017.
  14. ^ a b Brooks FP Jr. The Computer "Scientist" as Toolsmith: Studies in Interactive Computer Graphics. Proc. IFIP, 625-634 (1977).
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  16. ^ Barry CD, Bosshard HE, Ellis RA, Marshall GR (December 1974). "Evolving macromodular molecular modeling system". Fed. Proc. 33 (12): 2368–72. PMID 4435239.
  17. ^ Fritch, J. M., Ellis, R. A., Jacobi T. H., and Marshall, G. R. 1975. A Macromolecular Graphics System for Protein Structure Research. Computers and Graphics, 1, #2/3 (September), 271-278.
  18. ^ Cohen, G. H. and Feldmann, R. J. 1974. MAP - An Interactive Graphics Computer Program for the Manipulation and Fitting of Protein Molecules to Electron Density Maps. Am. Crystallography. Assoc. Spring 23, (Abstr.).
  19. ^ Stellman, S.D. (September 1975). "Application of three-dimensional interactive graphics in X-ray crystallographic analysis". Computers & Graphics. 1 (2–3): 279–288. doi:10.1016/0097-8493(75)90019-9.
  20. ^ Collins DM, Cotton FA, Hazen EE, Meyer EF, Morimoto CN (December 1975). "Protein crystal structures: quicker, cheaper approaches". Science. 190 (4219): 1047–53. Bibcode:1975Sci...190.1047C. doi:10.1126/science.1188383. PMID 1188383. S2CID 44583219.
  21. ^ Feldmann, R. J. 1976. AMSOM – Atlas of Macromolecular Structure on Microfiche.. Maryland: Tracor Jitco Inc.
  22. ^ Rosenberger, F. U., et al. 1976. Extracts from 1976 NIH Annual Report. Technical Memorandum No. 230, Computer Systems Laboratory, Washington University, St. Louis, Missouri.
  23. ^ Lipscomb, JS. Three-dimensional cues for a molecular computer graphics system. PhD Dissertation, University of North Carolina at Chapel Hill, North Carolina. (1981)
  24. ^ Britton E, Lipscomb JS, Pique ME, Wright, WV, Brooks FP Jr, Pique ME. The GRIP-75 Man-machine Interface. ACM SIGGRAPH Video Review, (4), (Aug. 1981).
  25. ^ Britton, E. G. 1977. A Methodology for the Ergonomic Design of Interactive Computer Graphics Systems, and its Application to Crystallography. PhD Dissertation, University of North Carolina, Chapel Hill, North Carolina.
  26. ^ Pique, M. E. 1980. Nested Dynamic Rotations for Computer Graphics. M. S. Thesis, University of North Carolina, Chapel Hill, North Carolina..
  27. ^ Tsernoglou D, Petsko GA, Tu AT (April 1977). "Protein sequencing by computer graphics". Biochim. Biophys. Acta. 491 (2): 605–8. doi:10.1016/0005-2795(77)90309-9. PMID 857910.
  28. ^ Jones, T.A. (August 1978). "A Graphics Model Building and Refinement System for Macromolecules". Journal of Applied Crystallography. 11 (4): 268–272. doi:10.1107/S0021889878013308.
  29. ^ Jones, T. A. 1978b. The RING [user manual]. Max-Planck-Institut fur Biochemie, 8033 Martinsried bei Muchen, Germany.
  30. ^ Diamond, R. 1978. Bilder. A computer graphics program for bipolymers and its application to interpretation of structure of tobacco mosaic virus protein disks at 2-A resolution. Proc. International Union of Pure and Applied Biochemistry: International Symposium on Structure, Conformation, Function, and Evolution. Madras, India, (4 January), Pergamon Press.
  31. ^ Abagyan R, Lee WH, Raush E, et al. (February 2006). "Disseminating structural genomics data to the public: from a data dump to an animated story". Trends Biochem. Sci. 31 (2): 76–8. doi:10.1016/j.tibs.2005.12.006. PMID 16406633.
  32. ^ Raush E, Totrov M, Marsden BD, Abagyan R (2009). "A new method for publishing three-dimensional content". PLOS ONE. 4 (10): e7394. Bibcode:2009PLoSO...4.7394R. doi:10.1371/journal.pone.0007394. PMC 2754609. PMID 19841676.
  33. ^ Smith, Thomas J. (27 October 2005). "Displaying and Analyzing Atomic Structures on the Macintosh". Danforth Plant Science Center. Archived from the original on 28 March 2002.

External links[edit]