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Molecular graphics

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Molecular graphics 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 artistically.[3]

History

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Prior to the use of computer graphics in representing molecular structure, Robert Corey and Linus Pauling developed a system for representing atoms or groups of atoms from hard wood on a scale of 1 inch = 1 angstrom connected by a clamping device to maintain the molecular configuration.[4] These early models also established the CPK coloring scheme that is still used today to differentiate the different types of atoms in molecular models (e.g. carbon = black, oxygen = red, nitrogen = blue, etc). This early model was improved upon in 1966 by W.L. Koltun and are now known as Corey-Pauling-Koltun (CPK) models.[5]

The earliest efforts to produce models of molecular structure was done by Project MAC using wire-frame models displayed on a cathode ray tube in the mid 1960s. In 1965, Carroll Johnson distributed the Oak Ridge thermal ellipsoid plot (ORTEP) that visualized molecules as a ball-and-stick model with lines representing the bonds between atoms and ellipsoids to represent the probability of thermal motion.[6] Thermal ellipsoid plots quickly became the de facto standard used in the display of X-ray crystallography data, and are still in wide use today.[6] The first practical use of molecular graphics was a simple display of the protein myoglobin using a wireframe representation in 1966 by Cyrus Levinthal and Robert Langridge working at Project MAC.[7]

Among the milestones in high-performance molecular graphics was the work of Nelson Max in "realistic" rendering of macromolecules using reflecting spheres.

 
A pair of CrystalEyes shutter glasses

Initially much of the technology concentrated on high-performance 3D graphics.[8] During the 1970s, methods for displaying 3D graphics using cathode ray tubes were developed using continuous tone computer graphics in combination with electro-optic shutter viewing devices.[9] The first devices used an active shutter 3D system, generating different perspective views for the left and right channel to provide the illusion of three-dimensional viewing. Stereoscopic viewing glasses were designed using lead lanthanum zirconate titanate (PLZT) ceramics as electronically-controlled shutter elements.[10] Active 3D glasses require batteries and work in concert with the display to actively change the presentation by the lenses to the wearer's eyes. Many modern 3D glasses use a passive, polarized 3D system that enables the wearer to visualize 3D effects based on their own perception. Passive 3D glasses are more common today since they are less expensive.[11]

The requirements of macromolecular crystallography also drove molecular graphics 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.

Timeline

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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[12] 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[13] 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 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[14] 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[15] 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[16] 1971 Adage AGT/50 display Interactive molecular structure viewing system. Mathematics of nested rotation and for laboratory-space rotation.
Perkins, Piper, Tattam, White[17] 1971 Honeywell DDP 516 computer, EAL TR48 analog computer, Lanelec oscilloscope, 7 linear potentiometers. Stereo. Interactive molecular structure viewing system.
Wright[18][19][20] 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[21] 1972 University of Oxford: 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 University of Leeds: 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:[22][23] Washington University in 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[24] 1974 DEC PDP-10 computer, Adage display, push buttons, keyboard, knobs Prototype large-molecule crystallographic structure solution system.
Stellman[25] 1975 Princeton University: 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,[26] 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.) University of California 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.[27]
Rosenberger et al. 1976 MMS-X:[28] Washington University in 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[20][29][30][31][32] 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.[33]
Jones 1978 FRODO and RING[34][35] 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[36] 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.[37][38]
ChemAxon 1998- MarvinSketch & MarvinView. MarvinSpace (2005) proprietary Java applet or stand-alone application.

Types

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Ball-and-stick models

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Main article: Ball-and-stick model
 
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

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Main article: Space-filling model
 
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. Atoms that share a bond overlap with each other.

Surfaces

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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 charge density.[39][40]

Ribbon diagrams

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Main article: Ribbon diagram
 
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.[41]

See also

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References

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  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. ^ Corey, Robert B.; Pauling, Linus (1953). "Molecular Models of Amino Acids, Peptides, and Proteins". Review of Scientific Instruments. 24 (8): 621. Bibcode:1953RScI...24..621C. doi:10.1063/1.1770803. Retrieved 13 June 2022.
  5. ^ Koltun, Walter L. (December 1965). "Precision space-filling atomic models". Biopolymers. 3 (6): 665–679. doi:10.1002/bip.360030606. PMID 4158989. S2CID 38806627.
  6. ^ a b Atwood, Jerry L.; Barbour, Leonard J. (2003). "Molecular Graphics: From Science to Art". Crystal Growth & Design. 3 (1): 3–8. doi:10.1021/cg020063o. Retrieved 13 June 2022.
  7. ^ Francoeur, Eric (2002). "Cyrus Levinthal, the Kluge and the origins of interactive molecular graphics". Endeavour. 26 (4): 127–131. doi:10.1016/S0160-9327(02)01468-0. PMID 12535918. Retrieved 13 June 2022.
  8. ^ Porter TK (August 1978). "Spherical shading". ACM SIGGRAPH Computer Graphics. 12 (3): 282–5. doi:10.1145/965139.639789.
  9. ^ 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.
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  11. ^ Wiley, Suzanne S. (12 May 2022). "What Are Passive 3D Glasses?". EasyTechJunkie. Retrieved 14 June 2022.
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  34. ^ 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.
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  36. ^ 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.
  37. ^ 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.
  38. ^ 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.
  39. ^ Wolfson, Haim; Duhovny, Dina; Tsherniak, Aviad. "Molecular Surface Representation". www.cs.tau.ac.il. Retrieved 14 June 2022.
  40. ^ O'Donnell, TJ. "The Science and Art of Molecular Surfaces". www.cs.uic.edu. Retrieved 14 June 2022.
  41. ^ 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.
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