Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. Ever since Dalton's atoms and Kekule'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. This article concentrates on the use of computers to create molecular graphics (often shortened to "MG" in this article). Note, however, that many molecular graphics programs and systems have close coupling between the graphics and editing commands or calculations such as in molecular modelling. In science, a molecule is a group of atoms in a definite arrangement held together by chemical bonds. ... John Dalton John Dalton (September 6, 1766 – July 27, 1844) was an English chemist and physicist, born at Eaglesfield, near Cockermouth in Cumberland. ... Friedrich August Kekulé von Stradonitz (September 7, 1829 - July 13, 1896) was a German organic chemist. ... Benzene, also known as benzol, is an organic chemical compound with the formula C6H6. ... The backbone dihedral angles are included in the molecular model of a protein. ...

Relation to molecular models

Fig. 1. Key: Hydrogen = white, carbon = grey, nitrogen = blue, oxygen = red, and phosphorus = orange.

There has been a long tradition of creating molecular models from physical materials. Perhaps the best known is Crick and Watson's model of DNA built from rods and planar sheets, but the most widely used approach is to represent all atoms and bonds explicitly using the "ball and stick" approach. This can demonstrate a wide range of properties, such as shape, relative size, and flexibility. Many chemistry courses expect that students will have access to ball and stick models. One goal of mainstream molecular graphics has been to represent the "ball and stick" model as realistically as possible and to couple this with calculations of molecular properties. Image File history File links No higher resolution available. ... Image File history File links No higher resolution available. ... General Name, Symbol, Number hydrogen, H, 1 Chemical series nonmetals Group, Period, Block 1, 1, s Appearance colorless Atomic mass 1. ... General Name, Symbol, Number carbon, C, 6 Chemical series nonmetals Group, Period, Block 14, 2, p Appearance black (graphite) colorless (diamond) Standard atomic weight 12. ... General Name, Symbol, Number nitrogen, N, 7 Chemical series nonmetals Group, Period, Block 15, 2, p Appearance colorless gas Standard atomic weight 14. ... General Name, Symbol, Number oxygen, O, 8 Chemical series nonmetals, chalcogens Group, Period, Block 16, 2, p Appearance colorless (gas) very pale blue (liquid) Standard atomic weight 15. ... General Name, Symbol, Number phosphorus, P, 15 Chemical series nonmetals Group, Period, Block 15, 3, p Appearance waxy white/ red/ black/ colorless Standard atomic weight 30. ... This page meets Wikipedias criteria for speedy deletion. ... Francis Harry Compton Crick OM FRS (8 June 1916 – 28 July 2004) was an English molecular biologist, physicist, and neuroscientist, who is most noted for being one of the co-discoverers of the structure of the DNA molecule in 1953. ... Sir James Dewey Watson KBE(Hon) ForMemRS (born April 6, 1928) is an American scientist, best known as one of the discoverers of the structure of the DNA molecule. ...

Figure 1 shows a small molecule (NH₃CH₂CH₂C(OH)(PO₃H)(PO₃H)-), as drawn by the Jmol program. It is important to realise that the colours are purely a convention. Molecules can never be visible under any light microscope and atoms are not coloured, do not have hard surfaces and do not reflect light. Bonds are not rod-shaped. If physical molecular models had not existed, it is unlikely that molecular graphics would currently use this metaphor. Jmol is molecule viewer for use in chemistry and biochemistry. ... A chemical bond is the physical process responsible for the attractive interactions between atoms and molecules, and that which confers stability to diatomic and polyatomic chemical compounds. ... This page meets Wikipedias criteria for speedy deletion. ...

Comparison of physical models with molecular graphics

Physical models and computer models have partially complementary strengths and weaknesses. Physical models can be used by those without access to a computer and now can be made cheaply out of plastic materials. Their tactile and visual aspects cannot be easily reproduced by computers (although haptic devices have occasionally been built). On a computer screen, the flexibility of molecules is also difficult to appreciate; illustrating the pseudorotation of cyclohexane is a good example of the value of mechanical models. Haptic, from the Greek αφή (Haphe), means pertaining to the sense of touch. ... The IUPAC defines pseudorotation as a conformational change resulting in a structure that appears to have been produced by rotation of the entire initial molecule and is superimposable on the initial one, unless different positions are distinguished by substitution or isotopic labeling. ... Cyclohexane is a cycloalkane with the molecular formula C6H12. ...

However, it is difficult to build large physical molecules, and all-atom physical models of even simple proteins could take weeks or months to build. Moreover, physical models are not robust and they decay over time. Molecular graphics is particularly valuable for representing global and local properties of molecules, such as electrostatic potential. Graphics can also be animated to represent molecular processes and chemical reactions, a feat that is not easy to reproduce physically.

History

Initially the rendering was on early CRT 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. Illustrations published in Scientific American in 1996 helped to popularise MG. Among the milestones in high-performance MG was the work of Nelson Max in "realistic" rendering of macromolecules using reflecting spheres. CRT can mean: Cathode Ray Tube, in electronics, a display device (such as those used in one type of television) C Run-Time, in computing Charitable Remainder Trust, in Law Chinese Remainder Theorem, in mathematics Corneal Refractive Therapy, in medicine Criterion-referenced test, in U.S. schools Critical race theory... This article or section does not cite its references or sources. ... Computer graphics is a sub-field of computer science and is concerned with digitally synthesizing and manipulating visual content. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Cyrus Levinthal (May 2, 1922–November 4, 1990) was an American molecular biologist. ... Scientific American is a popular-science magazine, published (first weekly and later monthly) since August 28, 1845, making it the oldest continuously published magazine in the United States. ... A macromolecule is a large molecule with a large molecular mass bonded covalently, but generally the use of the term is restricted to polymers and molecules which structurally include polymers. ... A sphere is a perfectly symmetrical geometrical object. ...

By about 1980 many laboratories both in academia and industry had recognized the power of the computer to analyse and predict the properties of molecules, especially in materials science and the pharmaceutical industry. The discipline was often called "molecular graphics" and in 1982 a group of academics and industrialists in the UK set up the Molecular Graphics Society (MGS). Initially much of the technology concentrated either on high-performance 3D graphics, including interactive rotation or 3D rendering of atoms as spheres (sometimes with radiosity). During the 1980s a number of programs for calculating molecular properties (such as molecular dynamics and quantum mechanics) became available and the term "molecular graphics" often included these. As a result the MGS has now changed its name to the Molecular Graphics and Modelling Society (MGMS). The Materials Science Tetrahedron, which often also includes Characterization at the center Materials science is an interdisciplinary field involving the properties of matter and its applications to various areas of science and engineering. ... This is a list of pharmaceutical and biotech companies that are major manufacturers on global or national markets : Abbott Laboratories Able Laboratories Akzo Nobel Allergan Almirall Prodesfarma Alphapharm Altana (previously Byk Gulden) ALZA, part of Johnson & Johnson Amgen AstraZeneca, formed from the merger of Astra AB and Zeneca Group PLC... The rewrite of this article is being devised at Talk:3D computer graphics/Temp. ... Radiosity is a global illumination algorithm used in 3D computer graphics rendering. ... Molecular dynamics (MD) is a form of computer simulation where atoms and molecules are allowed to interact for a period of time under known laws of physics. ... Fig. ...

The requirements of macromolecular crystallography also drove MG because the traditional techniques of physical model-building could not scale. 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. X-ray crystallography or single-crystal X-ray diffraction is an analytical technique which uses the diffraction pattern produced by bombarding a single crystal with X-rays to solve the crystal structure. ... Electron density is the measure of the probability of an electron being present at a specific location. ...

Art, science and technology in molecular graphics

Fig. 2. Image of hemagglutinin with alpha helices depicted as cylinders and the rest of the chain as silver coils. The individual protein atoms (several thousand) have been hidden. All of the non-hydrogen atoms in the two ligands (presumably sialic acid) have been shown near the top of the diagram. Key: Carbon = grey, oxygen = red, nitrogen = blue.

Both computer technology and graphic arts have contributed to molecular graphics. The development of structural biology in the 1950s led to a requirement to display molecules with thousands of atoms. The existing computer technology was limited in power, and in any case a naive depiction of all atoms left viewers overwhelmed. Most systems therefore used conventions where information was implicit or stylistic. Two vectors meeting at a point implied an atom or (in macromolecules) a complete residue (10-20 atoms). Image File history File links Hemagglutinin_molecule. ... Image File history File links Hemagglutinin_molecule. ... Hemagglutinin, as depicted in a simplified molecular model. ... This article is about the shape. ... In chemistry, a ligand is an atom, ion, or molecule (see also: functional group) that generally donates one or more of its electrons through a coordinate covalent bond to, or shares its electrons through a covalent bond with, one or more central atoms or ions (these ligands act as a... Sialic acid Sialic acid is a derivative of a nine-carbon monosaccharide, named from the Greek σιαλοσ (sialos) saliva. It is the negative charge of this chemical that is responsible for the slippery feel of saliva and mucins coating the body’s organs. ... General Name, Symbol, Number carbon, C, 6 Chemical series nonmetals Group, Period, Block 14, 2, p Appearance black (graphite) colorless (diamond) Standard atomic weight 12. ... General Name, Symbol, Number oxygen, O, 8 Chemical series nonmetals, chalcogens Group, Period, Block 16, 2, p Appearance colorless (gas) very pale blue (liquid) Standard atomic weight 15. ... General Name, Symbol, Number nitrogen, N, 7 Chemical series nonmetals Group, Period, Block 15, 2, p Appearance colorless gas Standard atomic weight 14. ... Structural biology is a branch of molecular biology concerned with the study of the architecture and shape of biological macromolecules--proteins and nucleic acids in particular—and what causes them to have the structures they have. ... Properties In chemistry and physics, an atom (Greek ἄτομος or átomos meaning indivisible) is the smallest particle still characterizing a chemical element. ... Example showing effect of vector graphics versus raster graphics. ... A residue, broadly, is anything left behind by a reaction or event. ...

The macromolecular approach was popularized by Dickerson and Geis' presentation of proteins and the graphic work of Jane Richardson through high-quality hand-drawn diagrams. In this they strove to capture the intrinsic 'meaning' of the molecule. This search for the "messages in the molecule" has always accompanied the increasing power of computer graphics processing. Typically the depiction would concentrate on specific areas of the molecule (such as the active site) and this might have different colours or more detail in the number of explicit atoms or the type of depiction (e.g., spheres for atoms). The active site of an enzyme is the binding site where catalysis occurs. ...

In some cases the limitations of technology have led to serendipitous methods for rendering. Most early graphics devices used vector graphics, which meant that rendering spheres and surfaces was impossible. Michael Connolly's program "MS" calculated points on the surface-accessible surface of a molecule, and the points were rendered as dots with good visibility using the new vector graphics technology, such as the Evans and Sutherland PS300 series. Thin sections ("slabs") through the structural display showed very clearly the complementarity of the surfaces for molecules binding to active sites, and the "Connolly surface" became a universal metaphor. Example showing effect of vector graphics versus raster graphics. ... On the left: nucleotides that forms the DNA and their complementary. ...

The relationship between the art and science of molecular graphics is shown in the exhibitions sponsored by the Molecular Graphics Society. Some exhibits are created with molecular graphics programs alone, while others are collages, or involve physical materials. An example from Mike Hann (1994), inspired by Magritte's painting Ceci n'est pas une pipe, shows an image of a salmeterol molecule (Figure 3). A collage composed of magazine articles and pictures Collage (From the French: , to stick) is regarded as a work of visual arts made from an assemblage of different forms, thus creating a new whole. ... René François Ghislain Magritte (November 21, 1898 - August 15, 1967) was a Surrealist artist, born in Lessines, Belgium. ... Salmeterol is a long-acting beta2-adrenergic receptor agonist drug that is currently prescribed for the treatment of asthma and chronic obstructive pulmonary disease COPD. It is currently available in both dry-powder inhalers (DPIs) and pressurised metered dose inhalers (pMDIs). ...

"Ceci n'est pas une molecule," writes Mike Hann, "serves to remind us that all of the graphics images presented here are not molecules, not even pictures of molecules, but pictures of icons which we believe represent some aspects of the molecule's properties." The image was generated in Insight II; the background and text were added using Adobe Photoshop. Insight: Insight is a piece of information. ... Adobe Photoshop, or simply Photoshop, is a graphics editor developed and published by Adobe Systems. ...

Space-filling models

Main article: Space-filling model

Fig. 4. Space-filling model of formic acid. Key: Hydrogen = white, carbon = black, oxygen = red.

Fig. 4 is a "space-filling" representation of formic acid, where atoms are drawn to suggest the amount of space they occupy. This is necessarily an icon: in the quantum mechanical representation of molecules, there are only (positively charged) nuclei and a "cloud" of negative electrons. The electron cloud defines an approximate size for the molecule, though there can be no single precise definition of size. For many years the size of atoms has been approximated by mechanical models (CPK), where the atoms have been represented by plastic spheres whose radius (van der Waals radius) describes a sphere within which "most" of the electron density can be found. These spheres could be clicked together to show the steric aspects of the molecule rather than the positions of the nuclei. Fig. 4 shows the intricacy required to make sure that all spheres intersect correctly, and also demonstrates a reflective model. This is a calotte model of cyclohexane. ... Image File history File links No higher resolution available. ... Image File history File links No higher resolution available. ... General Name, Symbol, Number hydrogen, H, 1 Chemical series nonmetals Group, Period, Block 1, 1, s Appearance colorless Atomic mass 1. ... General Name, Symbol, Number carbon, C, 6 Chemical series nonmetals Group, Period, Block 14, 2, p Appearance black (graphite) colorless (diamond) Standard atomic weight 12. ... General Name, Symbol, Number oxygen, O, 8 Chemical series nonmetals, chalcogens Group, Period, Block 16, 2, p Appearance colorless (gas) very pale blue (liquid) Standard atomic weight 15. ... Formic acid (systematically called methanoic acid) is the simplest carboxylic acid. ... e- redirects here. ... A way to color atoms when visualizing molecular models, inspired by CPK plastic molecule model kits by Corey, Pauling and Kultun. ... The van der Waals radius of an atom is the radius of an imaginary hard sphere which can be used to model the atom for many purposes. ... Steric effects are the interaction of molecules dictated by their shape and/or spatial relationships. ...

Fig. 5. A molecule (zirconocene) where part (left) is rendered as ball-and-stick and part (right) as an isosurface.

Since the atomic radii (e.g. in Fig. 4) are only slightly less than the distance between bonded atoms, the iconic spheres intersect, and in the CPK models, this was achieved by planar truncations along the bonding directions, the section being circular. When raster graphics became affordable, one of the common approaches was to replicate CPK models in silico. It is relatively straightforward to calculate the circles of intersection, but more complex to represent a model with hidden surface removal. A useful side product is that a conventional value for the molecular volume can be calculated. Isosurface around Zirconocene molecule. ... Isosurface around Zirconocene molecule. ... Suppose the smiley face in the top left corner is an RGB bitmap image. ... in silico is an expression used to mean performed on computer or via computer simulation. ...

The use of spheres is often for convenience, being limited both by graphics libraries and the additional effort required to compute complete electronic density or other space-filling quantities. It is now relatively common to see images of isosurfaces that have been coloured to show quantities such as electrostatic potential. The commonest isosurfaces are the Connolly surface, or the volume within which a given proportion of the electron density lies. The isosurface in Fig. 5 appears to show the electrostatic potential, with blue colours being negative and red/yellow (near the metal) positive. (There is no absolute convention of colouring, and red/positive, blue/negative are often confusingly reversed!) Opaque isosurfaces do not allow the atoms to be seen and identified and it is not easy to deduce them. Because of this, isosurfaces are often drawn with a degree of transparency. Zirconocene with an isosurface showing areas of the molecule susceptible to electrophilic attack. ... Electric potential is the potential energy per unit charge associated with a static (time-invariant) electric field, also called the electrostatic potential, typically measured in volts. ...

Technology

Molecular graphics has always pushed the limits of display technology, and has seen a number of cycles of integration and separation of compute-host and display. Early systems like Project MAC were bespoke and unique, but in the 1970s the MMS-X and similar systems used (relatively) low-cost terminals, such as the Tektronix 4014 series, often over dial-up lines to multi-user hosts. The devices could only display static pictures but, were able to evangelize MG. In the late 1970s, it was possible for departments (such as crystallography) to afford their own hosts (e.g., PDP-11) and to attach a display (such as Evans & Sutherland's MPS) directly to the bus. The display list was kept on the host, and interactivity was good since updates were rapidly reflected in the display—at the cost of reducing most machines to a single-user system. Bespoke is a usually British English term for clothing made at a customers behest, and exactly to the customers specification. ... The Tektronix 4014 was an early text and graphics computer terminal based on the companys own storage tube technology. ... In telecommunication, the term dial-up has the following meanings: Dial-up access, typically to the Internet A service feature in which a user initiates service on a previously arranged trunk or transfers, without human intervention, from an active trunk to a standby trunk. ... The PDP-11 was a 16-bit minicomputer sold by Digital Equipment Corp. ... Evans & Sutherland is a computer firm involved in the computer graphics field. ... In computer architecture, a bus is a subsystem that transfers data or power between computer components inside a computer or between computers and typically is controlled by device driver software. ... Display list - a group of GL (graphics language, e. ...

In the early 1980s, Evans & Sutherland (E&S) decoupled their PS300 display, which contained its own display information transformable through a dataflow architecture. Complex graphical objects could be downloaded over a serial line (e.g. 9600 baud) and then manipulated without impact on the host. The architecture was excellent for high performance display but very inconvenient for domain-specific calculations, such as electron-density fitting and energy calculations. Many crystallographers and modellers spent arduous months trying to fit such activities into this architecture. It has been suggested that this article or section be merged with Dataflow architecture. ... A male DE-9 serial port on the rear panel of a PC. In computing, a serial port consists of an interface on a computer system through which information transfers in or out one bit at a time (contrast parallel port). ... In telecommunications and electronics, baud (pronounced , unit symbol Bd), is a measure of the symbol rate; that is, the number of distinct symbol changes (signalling events) made to the transmission medium per second in a digitally modulated signal. ...

The benefits for MG were considerable, but by the later 1980s, UNIX workstations such as SUN-3 with raster graphics (initially at a resolution of 256 by 256) had started to appear. Computer-assisted drug design in particular required raster graphics for the display of computed properties such as atomic charge and electrostatic potential. Although E&S had a high-end range of raster graphics (primarily aimed at the aerospace industry) they failed to respond to the low-end market challenge where single users, rather than engineering departments, bought workstations. As a result the market for MG displays passed to Silicon Graphics, coupled with the development of minisupercomputers (e.g., CONVEX and Alliant) which were affordable for well-supported MG laboratories. Silicon Graphics provided a graphics language, IrisGL, which was easier to use and more productive than the PS300 architecture. Commercial companies (e.g., Biosym, Polygen/MSI) ported their code to Silicon Graphics, and by the early 1990s, this was the "industry standard". Filiation of Unix and Unix-like systems Unix (officially trademarked as UNIX®) is a computer operating system originally developed in the 1960s and 1970s by a group of AT&T employees at Bell Labs including Ken Thompson, Dennis Ritchie and Douglas McIlroy. ... A computer workstation, often colloquially referred to as workstation, is a high-end general-purpose microcomputer designed to be used by one person at a time and which offers higher performance than normally found in a personal computer, especially with respect to graphics, processing power and the ability to carry... The Sun is the star at the center of the Solar System. ... Suppose the smiley face in the top left corner is an RGB bitmap image. ... Image resolution describes the detail an image holds. ... Drug design is the approach of finding drugs by design, based on their biological targets. ... Electric charge is a fundamental conserved property of some subatomic particles, which determines their electromagnetic interaction. ... Electric potential is the potential energy per unit charge associated with a static (time-invariant) electric field, also called the electrostatic potential, typically measured in volts. ... Look up aerospace in Wiktionary, the free dictionary. ... Silicon Graphics, Inc. ... Minisupercomputers constituted a class of computers that emerged in the mid-1980s. ... Convex Computer was a company that produced a number of vector minisupercomputers, supercomputers for small-to-medium-sized businesses. ... Alliant Computer Systems was a computer company that designed and manufactured parallel computing systems. ...

Stereoscopic displays were developed based on liquid crystal polarized spectacles, and while this had been very expensive on the PS300, it now became a commodity item. A common alternative was to add a polarizable screen to the front of the display and to provide viewers with extremely cheap spectacles with orthogonal polarization for separate eyes. With projectors such as Barco, it was possible to project stereoscopic display onto special silvered screens and supply an audience of hundreds with spectacles. In this way molecular graphics became universally known within large sectors of chemical and biochemical science, especially in the pharmaceutical industry. Because the backgrounds of many displays were black by default, it was common for modelling sessions and lectures to be held with almost all lighting turned off. Stereopsis (from stereo meaning solidity, and opsis meaning vision or sight) is the process in visual perception leading to perception of stereoscopic depth. ... Schlieren texture of Liquid Crystal nematic phase Liquid crystals are substances that exhibit a phase of matter that has properties between those of a conventional liquid, and those of a solid crystal. ... This article treats polarization in electrodynamics. ... In mathematics, orthogonal is synonymous with perpendicular when used as a simple adjective that is not part of any longer phrase with a standard definition. ... Barco N.V. (Euronext: BAR) is a display hardware manufacturer specialising in CRT projectors, LCD projectors, DLP projectors, LED displays and flat panel displays. ...

In the last decade almost all of this technology has become commoditized. IrisGL evolved to OpenGL so that molecular graphics can be run on any machine. In 1992, Roger Sayle released his RasMol program into the public domain. RasMol contained a very high-performance molecular renderer that ran on Unix/X Window, and Sayle later ported this to the Windows and Macintosh platforms. The Richardsons developed Kinemage, which was also multi-platform. By specifying the chemical MIME type, molecular models could be served over the Internet, so that for the first time MG could be distributed at zero cost regardless of platform. In 1995, Birkbeck College's crystallography department used this to run "Principles of Protein Structure", the first multimedia course on the Internet, which reached 100 to 200 scientists. OpenGL (Open Graphics Library) is a standard specification defining a cross-language cross-platform API for writing applications that produce 3D computer graphics (and 2D computer graphics as well). ... RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank. ... Rendering is the process of generating an image from a model, by means of a software program. ... In computing, the X Window System (commonly X11 or X) is a windowing system for bitmap displays. ... Microsoft Windows is the name of several families of proprietary software operating systems by Microsoft. ... The first Macintosh computer, introduced in 1984, upgraded to a 512K Fat Mac. The Macintosh or Mac, is a line of personal computers designed, developed, manufactured, and marketed by Apple Computer. ... A kinemage (also called kinetic image) is an interactive graphic scientific illustration. ... Multipurpose Internet Mail Extensions (MIME) is an Internet Standard for the format of e-mail. ... Birkbeck, University of London, sometimes referred to by its former name Birkbeck College or by the abbreviation BBK, is a College of the University of London. ...

Fig. 6. A molecule of porin shown without ambient occlusion (left) and with (right). Advanced rendering effects can improve the comprehension of the 3D shape of a molecule.

MG continues to see innovation that balances technology and art, and currently zero-cost or open source programs such as PyMOL and Jmol have very wide use and acceptance. Image File history File links Size of this preview: 566 × 599 pixelsFull resolution (677 × 717 pixel, file size: 362 KB, MIME type: image/png) File links The following pages on the English Wikipedia link to this file (pages on other projects are not listed): Molecular graphics ... Image File history File links Size of this preview: 566 × 599 pixelsFull resolution (677 × 717 pixel, file size: 443 KB, MIME type: image/png) File links The following pages on the English Wikipedia link to this file (pages on other projects are not listed): Molecular graphics ... Porins are transmembrane proteins that are large enough to facilitate passive diffusion. ... Ambient occlusion is a shading method used in 3D computer graphics which can help add realism by taking into account attenuation of light caused by obstructive geometry. ... Open source refers to projects that are open to the public and which draw on other projects that are freely available to the general public. ... PyMOL is an open-source, user-sponsored, molecular visualization system created by Warren Lyford DeLano and commercialized by DeLano Scientific LLC, which is a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. ... Jmol is molecule viewer for use in chemistry and biochemistry. ...

Recently the wide spread diffusion of advanced graphics hardware, has improved the rendering capabilities of the visualization tools. The capabilites of current shading languages allow the inclusion of advanced graphic effects (like ambient occlusion, cast shadows and non-photorealistic rendering techniques) in the interactive visualization of molecules. These graphic effects, beside being eye candy, can improve the comprehension of the threedimensional shapes of the molecules. An example of the effects that can be achieved exploiting recent graphics hardware can be seen in the simple open source visualization system QuteMol. A graphics card, video card, v card, video board, video display board, display adapter, video adapter, or graphics adapter [1] is a computer component designed to convert the logical representation of visual information into a signal that can be used as input for a display medium. ... A Shader in the field of computer graphics is a set of software instructions, which is used by the graphic resources primarily to perform rendering effects. ... Ambient occlusion is a shading method used in 3D computer graphics which can help add realism by taking into account attenuation of light caused by obstructive geometry. ... Shadows on pavement A shadow is a region of darkness where light is blocked. ... Non-photorealistic rendering (NPR) is an area of computer graphics that focuses on enabling a wide variety of expressive styles for digital art. ... Eye candy is an expression used to describe something that is most remarkable by its appearance, but that doesnt have anything else so exciting. ... QuteMol QuteMol is an open source, interactive, high quality molecular visualization system. ...

Algorithms

Reference frames

Drawing molecules requires a transformation between molecular coordinates (usually, but not always, in Angstrom units) and the screen. Because many molecules are chiral it is essential that the handedness of the system (almost always right-handed) is preserved. In molecular graphics the origin (0, 0) is usually at the lower left, while in many computer systems the origin is at top left. If the z-coordinate is out of the screen (towards the viewer) the molecule will be referred to right-handed axes, while the screen display will be left-handed. An angstrom, angström, or ångström (symbol Å) is a unit of length. ... The term chiral (pronounced ) is used to describe an object which is non-superimposable on its mirror image. ...

Molecular transformations normally require:

• scaling of the display (but not the molecule).
• translations of the molecule and objects on the screen.
• rotations about points and lines.

Conformational changes (e.g. rotations about bonds) require rotation of one part of the molecule relative to another. The programmer must decide whether a transformation on the screen reflects a change of view or a change in the molecule or its reference frame.

Simple

Fig. 7. Stick model of caffeine drawn in Jmol.

In early displays only vectors could be drawn e.g. (Fig. 7) which are easy to draw because no rendering or hidden surface removal is required. Image File history File links No higher resolution available. ... Image File history File links No higher resolution available. ...

On vector machines the lines would be smooth but on raster devices Bresenham's algorithm is used (note the "jaggies" on some of the bonds, which can be largely removed with antialiasing software.) Bresenhams line algorithm is an algorithm that determines which points in an n-dimensional raster should be plotted in order to form a close approximation to a straight line between two given points. ... In digital signal processing, anti-aliasing is the technique of minimizing aliasing when representing a high-resolution signal at a lower resolution. ...

Atoms can be drawn as circles, but these should be sorted so that those with the largest z-coordinates (nearest the screen) are drawn last. Although imperfect, this often gives a reasonably attractive display. Other simple tricks which do not include hidden surface algorithms are:

• colouring each end of a bond with the same colour as the atom to which it is attached (Fig. 7).
• drawing less than the whole length of the bond (e.g. 10%-90%) to simulate the bond sticking out of a circle.
• adding a small offset white circle within the circle for an atom to simulate reflection.

Typical pseudocode for creating Fig. 7 (to fit the molecule exactly to the screen): Pseudocode (derived from pseudo and code) is a compact and informal high-level description of a computer programming algorithm that uses the structural conventions of programming languages, but omits detailed subroutines, variable declarations or language-specific syntax. ...

 // assume: // atoms with x, y, z coordinates (Angstrom) and elementSymbol // bonds with pointers/references to atoms at ends // table of colours for elementTypes // find limits of molecule in molecule coordinates as xMin, yMin, xMax, yMax scale = min(xScreenMax/(xMax-xMin), yScreenMax/(yMax-yMin)) xOffset = -xMin * scale; yOffset = -yMin * scale for (bond in $bonds) { atom0 = bond.getAtom(0) atom1 = bond.getAtom(1) x0 = xOffset+atom0.getX()*scale; y0 = yOffset+atom0.getY()*scale // (1) x1 = xOffset+atom1.getX()*scale; y1 = yOffset+atom1.getY()*scale // (2) x1 = atom1.getX(); y1 = atom1.getY() xMid = (x0 + x1) /2; yMid = (y0 + y1) /2; colour0 = ColourTable.getColour(atom0.getSymbol()) drawLine(colour0, x0, y0, xMid, yMid) colour1 = ColourTable.getColour(atom1.getSymbol()) drawLine(colour1, x1, y1, xMid, yMid) } 

Note that this assumes the origin is in the bottom left corner of the screen, with Y up the screen. Many graphics systems have the origin at the top left, with Y down the screen. In this case the lines (1) and (2) should have the y coordinate generation as:

 y0 = yScreenMax -(yOffset+atom0.getY()*scale) // (1) y1 = yScreenMax -(yOffset+atom1.getY()*scale) // (2) 

Changes of this sort change the handedness of the axes so it is easy to reverse the chirality of the displayed molecule unless care is taken.

Advanced

For greater realism and better comprehension of the 3D structure of a molecule many computer graphics algorithms can be used. For many years molecular graphics has stressed the capabilities of graphics hardware and has required hardware-specific approaches. With the increasing power of machines on the desktop, portability is more important and programs such as Jmol have advanced algorithms that do not rely on hardware. On the other hand recent graphics hardware is able to interactively render very complex molecule shapes with a quality that would not be possible with standard software techniques. Computer graphics is a sub-field of computer science and is concerned with digitally synthesizing and manipulating visual content. ... Jmol is molecule viewer for use in chemistry and biochemistry. ...

Chronology

This table provides an incomplete chronology of molecular graphics advances.

Cyrus Levinthal (May 2, 1922–November 4, 1990) was an American molecular biologist. ... The PDP-11 was a 16-bit minicomputer sold by Digital Equipment Corp. ... Tektronix is a United States corporation that is currently a major presence in the test, measurement, and measuring industry. ... It has been suggested that this article or section be merged into Data terminal. ... Silicon Graphics, Inc. ... The Sun is the star at the center of the Solar System. ... OpenGL (Open Graphics Library) is a specification defining a cross-language cross-platform API for writing applications that produce 3D computer graphics (and 2D computer graphics as well). ... RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank. ... A kinemage (also called kinetic image) is an interactive graphic scientific illustration. ... Elsevier MDL is a subsidiary of Elsevier. ... MDL Chime is a plugin used by web browsers to display the three dimensional structures of molecules. ... Jmol is molecule viewer for use in chemistry and biochemistry. ... PyMOL is an open-source, user-sponsored, molecular visualization system created by Warren Lyford DeLano and commercialized by DeLano Scientific LLC, which is a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. ... It has been suggested that Open source culture be merged into this article or section. ... The Java platform is the name for a computing environment, or platform, from Sun Microsystems which can run applications developed using the Java programming language and set of development tools. ... An applet is a software component that runs in the context of another program, for example a web browser. ... Stand-alone is a loosely defined term used to sort computer programs. ...

References

• Dickerson, R.E., and Geis, I., The structure and action of proteins. W.A. Benjamin: Menlo Park, CA, 1969.

See also

Wikimedia Commons has media related to:

Molecules

• Molecular model
• Molecular geometry

Image File history File links Commons-logo. ... Wikimedia Commons logo by Reid Beels The Wikimedia Commons (also called Commons or Wikicommons) is a repository of free content images, sound and other multimedia files. ... This page meets Wikipedias criteria for speedy deletion. ... Geometry of the water molecule Molecular geometry or molecular structure is the three dimensional arrangement of the atoms that constitute a molecule, inferred from the spectroscopic studies of the compound. ...

External links

History

• History of Visualization of Biological Macromolecules by Eric Martz and Eric Francoeur.
• Brief History of Molecular Mechanics/Graphics in LSU CHEM7770 lecture notes.
• Historical slides from Robert (Bob) Langridge. These show the influence of Crick and Watson on molecular graphics (including Levinthal's) and the development of early display technology, finishing with displays which were common in the mid-1980s on machines such as Evans and Sutherland's PS300 series.

Louisiana State University and Agricultural and Mechanical College at Baton Rouge, generally known as Louisiana State University or LSU, is a public, coeducational university located in Baton Rouge, Louisiana and the main campus of the Louisiana State University System. ...

People

• Interview with Langridge. The display looking down the axis of B-DNA has been likened to a rose window.
• Nelson Max's home page with links to 1982 classics.

The rose window in Bristol Cathedral, Bristol, England, at the western end of the nave. ...

Software and imagery

• Jmol home page contains an applet with an automatic display of many features of molecular graphics including metaphors, scripting, annotation and animation.

• Richardson Lab includes Kinemage and molecular graphics images.
• History of RasMol.
• Molecule of the Month at RCSB/PDB.
• Exhibitions of Molecular Graphics Art, 1994, 1998.

Publications and organizations

• Molecular Graphics and Modelling Society.
• Journal of Molecular Graphics and Modelling (formally Journal of Molecular Graphics). This journal is not open access.