Molecular graphics Totally Explained

Everything about Molecular Graphics totally explained

Molecular graphics (often shortened to "MG" in this article) is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". 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. 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.

Relation to molecular models

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. 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, don't have hard surfaces and don't reflect light. Bonds are not rod-shaped. If physical molecular models hadn't existed, it's unlikely that molecular graphics would currently use this metaphor.

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 can't 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.
However, it's 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 isn't 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. Among the milestones in high-performance MG was the work of Nelson Max in "realistic" rendering of macromolecules using reflecting spheres.
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 requirements of macromolecular crystallography also drove MG because the traditional techniques of physical model-building couldn't 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.

Art, science and technology in molecular graphics

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).
   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 (for example, spheres for atoms).
   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.
   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, uses an image of a salmeterol molecule.
"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."

Space-filling models

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.
Since the atomic radii (for example 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.
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 don't allow the atoms to be seen and identified and it isn't easy to deduce them. Because of this, isosurfaces are often drawn with a degree of transparency.

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 (for example, 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.
   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 (for example 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.
   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 (for example, 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 (for example, Biosym, Polygen/MSI) ported their code to Silicon Graphics, and by the early 1990s, this was the "industry standard". 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.
   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.


Fig. 6. A molecule of Porin (protein) 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.
Recently the wide spread diffusion of advanced graphics hardware, has improved the rendering capabilities of the visualization tools. The capabilities 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 three dimensional 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.

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's 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.
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 (for example 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

In early displays only vectors could be drawn for example (Fig. 7) which are easy to draw because no rendering or hidden surface removal is required.
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.)
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 don't include hidden surface algorithms are:

colouring each end of a bond with the same colour as the atom to which it's attached (Fig. 7).

drawing less than the whole length of the bond (for example 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):
// 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)
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's 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 don't rely on hardware. On the other hand recent graphics hardware is able to interactively render very complex molecule shapes with a quality that wouldn't be possible with standard software techniques.

Chronology

This table provides an incomplete chronology of molecular graphics advances.

Developer(s)	Approximate date	Technology	Comments
Crystallographers	< 1960	Hand-drawn	Crystal structures, with hidden atom and bond removal. Often clinographic projections.
Cyrus Levinthal, Bob Langridge	1960s	CRT	First protein display on screen (Project MAC).
Johnson, Motherwell	ca 1970	Pen plotter	ORTEP, PLUTO. Very widely deployed for publishing crystal structures.
Langridge, White, Marshall	Late 1970's	Departmental systems (PDP-11, Tektronix displays or DEC-VT11, for example MMS-X)	Mixture of commodity computing with early displays.
T. Alwyn Jones	1978	FRODO	Crystallographic structure solution.
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 -	1989, 2000	Machine independent	Nearly free, multifunctional, still fully supported, many free 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
Community efforts	2000-	Jmol, PyMol, Protein Workshop (www.pdb.org)	Open-source Java applet or stand-alone application.
San Diego Supercomputer Center	2006-	Sirius	Free for academic/non-profit institutions
NOCH	2002-	NOC	Powerful and open source code molecular structure explorer
Weizmann Institute of Science - Community efforts	2008-	Proteopedia	Collaborative, 3D wiki encyclopedia of proteins & other molecules

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