Molecular graphics

Last updated • 4 min readFrom Wikipedia, The Free Encyclopedia

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.

Contents

Colour molecular graphics are often used on chemistry journal covers artistically. [3]

History

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 CrystalEyes shutter glasses.jpg
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

Developer(s)Approximate dateTechnologyComments
Crystallographers< 1960Hand-drawnCrystal structures, with hidden atom and bond removal. Often clinographic projections.
Johnson, Motherwellc.1970Pen plotterORTEP, PLUTO. Very widely deployed for publishing crystal structures.
Cyrus Levinthal, Bob Langridge, Ward, Stots [12] 1966Project 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] 1969LINC 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.
Ortony1971Designed 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] 1971Light 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] 1971CHEMAST: 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] 1971Adage AGT/50 displayInteractive molecular structure viewing system. Mathematics of nested rotation and for laboratory-space rotation.
Perkins, Piper, Tattam, White [17] 1971Honeywell DDP 516 computer, EAL TR48 analog computer, Lanelec oscilloscope, 7 linear potentiometers. Stereo.Interactive molecular structure viewing system.
Wright [18] [19] [20] 1972GRIP-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, WatsonEarly 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, Jacobi1974MMS-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] 1974DEC PDP-10 computer, Adage display, push buttons, keyboard, knobsPrototype large-molecule crystallographic structure solution system.
Stellman [25] 1975 Princeton University: PDP-10 computer, LDS-1 display, knobsPrototype 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, Morimoto1975CRYSNET, [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 Kraut1976 (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 Porter1976NIH: 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.1976MMS-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 1977GRIP-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]
Jones1978FRODO 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.
Diamond1978Bilder [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, MarshallLate 1970sDepartmental systems (PDP-11, Tektronix displays or DEC-VT11, e.g. MMS-X)Mixture of commodity computing with early displays.
Davies, HubbardMid-1980sCHEM-X, HYDRALaboratory systems with multicolor, raster and vector devices (Sigmex, PS300).
Biosym, Tripos, PolygenMid-1980sPS300 and lower cost dumb terminals (VT200, SIGMEX)Commercial integrated modelling and display packages.
Silicon Graphics, Sun Late 1980s IRIS GL (UNIX) workstationsCommodity-priced single-user workstations with stereoscopic display.
EMBL - WHAT IF 1989, 2000Machine independentNearly free, multifunctional, still fully supported, many free servers based on it
Sayle, Richardson1992, 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
MolSoft1997–presentICM-Browserproprietary; free download for Windows, Mac, and Linux. [37] [38]
1998-MarvinSketch & MarvinView. MarvinSpace (2005)proprietary Java applet or stand-alone application.

Types

Ball-and-stick models

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. Jmol1.png
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

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

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. Water-elpot-transparent-3D-balls.png
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

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. Hemagglutinin molecule.png
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

Related Research Articles

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Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids. Crystallography is a fundamental subject in the fields of materials science and solid-state physics. The word crystallography is derived from the Ancient Greek word κρύσταλλος, and γράφειν. In July 2012, the United Nations recognised the importance of the science of crystallography by proclaiming that 2014 would be the International Year of Crystallography.

<span class="mw-page-title-main">Structural biology</span> Study of molecular structures in biology

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<span class="mw-page-title-main">X-ray crystallography</span> Technique used for determining crystal structures and identifying mineral compounds

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<span class="mw-page-title-main">BALL</span>

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<span class="mw-page-title-main">Frederic M. Richards</span> American biochemist and biophysicist (1925–2009)

Frederic Middlebrook Richards, commonly referred to as Fred Richards, was an American biochemist and biophysicist known for solving the pioneering crystal structure of the ribonuclease S enzyme in 1967 and for defining the concept of solvent-accessible surface. He contributed many key experimental and theoretical results and developed new methods, garnering over 20,000 journal citations in several quite distinct research areas. In addition to the protein crystallography and biochemistry of ribonuclease S, these included solvent accessibility and internal packing of proteins, the first side-chain rotamer library, high-pressure crystallography, new types of chemical tags such as biotin/avidin, the nuclear magnetic resonance (NMR) chemical shift index, and structural and biophysical characterization of the effects of mutations.

<span class="mw-page-title-main">Space-filling model</span> Type of 3D molecular model

In chemistry, a space-filling model, also known as a calotte model, is a type of three-dimensional (3D) molecular model where the atoms are represented by spheres whose radii are proportional to the radii of the atoms and whose center-to-center distances are proportional to the distances between the atomic nuclei, all in the same scale. Atoms of different chemical elements are usually represented by spheres of different colors.

<span class="mw-page-title-main">Jane S. Richardson</span> American biophysicist

Jane Shelby Richardson is an American biophysicist best known for developing the Richardson diagram, or ribbon diagram, a method of representing the 3D structure of proteins. Ribbon diagrams have become a standard representation of protein structures that has facilitated further investigation of protein structure and function globally. With interests in astronomy, math, physics, botany, and philosophy, Richardson took an unconventional route to establishing a science career. Richardson is a professor in biochemistry at Duke University.

<span class="mw-page-title-main">Ribbon diagram</span> 3D schematic representation of protein structure

Ribbon diagrams, also known as Richardson diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon depicts the general course and organisation of the protein backbone in 3D and serves as a visual framework for hanging details of the entire atomic structure, such as the balls for the oxygen atoms attached to myoglobin's active site in the adjacent figure. Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone. α-helices are shown as coiled ribbons or thick tubes, β-sheets 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.

Resolution in the context of structural biology is the ability to distinguish the presence or absence of atoms or groups of atoms in a biomolecular structure. Usually, the structure originates from methods such as X-ray crystallography, electron crystallography, or cryo-electron microscopy. The resolution is measured of the "map" of the structure produced from experiment, where an atomic model would then be fit into. Due to their different natures and interactions with matter, in X-ray methods the map produced is of the electron density of the system, whereas in electron methods the map is of the electrostatic potential of the system. In both cases, atomic positions are assumed similarly.

<span class="mw-page-title-main">Coot (software)</span>

The program Coot is used to display and manipulate atomic models of macromolecules, typically of proteins or nucleic acids, using 3D computer graphics. It is primarily focused on building and validation of atomic models into three-dimensional electron density maps obtained by X-ray crystallography methods, although it has also been applied to data from electron microscopy.

<span class="mw-page-title-main">Structure validation</span> Process of evaluating 3-dimensional atomic models of biomacromolecules

Macromolecular structure validation is the process of evaluating reliability for 3-dimensional atomic models of large biological molecules such as proteins and nucleic acids. These models, which provide 3D coordinates for each atom in the molecule, come from structural biology experiments such as x-ray crystallography or nuclear magnetic resonance (NMR). The validation has three aspects: 1) checking on the validity of the thousands to millions of measurements in the experiment; 2) checking how consistent the atomic model is with those experimental data; and 3) checking consistency of the model with known physical and chemical properties.

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