28.07.2019

Pymol Molecular Graphics System .psw In Powerpoint For Mac

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  1. Pymol Molecular Graphics System .psw In Powerpoint For Mac Free
  2. Pymol Molecular Graphics System .psw In Powerpoint For Mac 2016

My PyMol models and figures Figures from a recent publication – The Dinosaurs of the complement system The below figure is created from two manual build PDB models: the large membrane floor and the “dinosaurs” or rather the MBL oligomer of the lectin pathway.

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Pymol molecular graphics system .psw in powerpoint for mac

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Molecular graphics ( MG) is the discipline and philosophy of studying and their properties through graphical representation. Limits the definition to representations on a 'graphical display device'. Ever since 's atoms and's, 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. Key: = white, = grey, = blue, = red, and = orange. There has been a long tradition of creating from physical materials.

Perhaps the best known is and 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 ' 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 ( NH 3CH 2CH 2C(OH)(PO 3H)(PO 3H)-), as drawn by the program. It is important to realize that the colors and shapes are purely a convention, as individual atoms are not colored, nor do they have hard surfaces. between atoms are also not rod-shaped. 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 devices have occasionally been built).

On a computer screen, the flexibility of molecules is also difficult to appreciate; illustrating the of is a good example of the value of mechanical models. 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 screens or through drawing on paper.

Molecular structures have always been an attractive choice for developing new 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 molecule (Project MAC, 1966) by and Robert Langridge. Among the milestones in high-performance MG was the work of in 'realistic' rendering of using reflecting. 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 and the. 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, including interactive rotation or 3D rendering of atoms as spheres (sometimes with ). During the 1980s a number of programs for calculating molecular properties (such as and ) 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 also drove MG because the traditional techniques of physical model-building could not scale. The first two protein structures solved by molecular graphics without the aid of the Richards' Box were built with Stan Swanson's program FIT on the Vector General graphics display in the laboratory of Edgar Meyer at Texas A&M University: First Marge Legg in Al Cotton's lab at A&M solved the 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 determined from X-ray crystallography and the hypothetical molecular structure. In 2009 became the first software to use for molecular graphics.

Art, science and technology in molecular graphics. Image of with alpha 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 (presumably ) have been shown near the top of the diagram.

Key: = grey, = red, = blue. Both computer technology and graphic arts have contributed to molecular graphics. The development of in the 1950s led to a requirement to display molecules with thousands of. 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 meeting at a point implied an atom or (in macromolecules) a complete (10-20 atoms). The macromolecular approach was popularized by Dickerson and Geis' presentation of proteins and the graphic work of through high-quality hand-drawn diagrams such as the representation.

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 ) and this might have different colors or more detail in the number of explicit atoms or the type of depiction (e.g., spheres for atoms). In some cases the limitations of technology have led to serendipitous methods for rendering. Most early graphics devices used, 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 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, or involve physical materials. An example from Mike Hann (1994), inspired by painting Ceci n'est pas une pipe, uses an image of a 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. Space-filling model of formic acid. Key: = white, = black, = red.

4 is a 'space-filling' representation of, where atoms are drawn as solid spheres to suggest the space they occupy. This and all space-filling models are necessarily icons or abstractions: atoms are nuclei with of varying density surrounding them, and as such have no actual surfaces.

Pymol Molecular Graphics System .psw In Powerpoint For Mac Free

For many years the size of atoms has been approximated by physical models in which the volumes of plastic balls describe where much of the electron density is to be found (often sized to ). That is, the surface of these models is meant to represent a specific level of of the electron cloud, not any putative physical surface of the atom. A molecule (zirconocene) where part (left) is rendered as ball-and-stick and part (right) as an isosurface. Since the atomic radii (e.g. 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 became affordable, one of the common approaches was to replicate CPK models.

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 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 surfaces that have been colored to show quantities such as. Common surfaces in molecular visualization include,. The isosurface in Fig.

5 appears to show the electrostatic potential, with blue colors being negative and red/yellow (near the metal) positive (there is no absolute convention of coloring, and red/positive, blue/negative are often 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.

Technology Early interactive molecular computer graphics systems were machines, which used stroke-writing, sometimes even oscilloscopes. The electron beam does not sweep left-and-right as in a raster display. The display hardware followed a sequential list of digital drawing instructions (the display list), directly drawing at an angle one stroke for each molecular bond. When the list was complete, drawing would begin again from the top of the list, so if the list was long (a large number of molecular bonds), the display would flicker heavily. Later vector displays could rotate complex structures with smooth motion, since the orientation of all of the coordinates in the display list could be changed by loading just a few numbers into rotation registers in the display unit, and the display unit would multiply all coordinates in the display list by the contents of these registers as the picture was drawn. The early black-and white vector displays could somewhat distinguish for example a molecular structure from its surrounding electron density map for crystallographic structure solution work by drawing the molecule brighter than the map. Color display makes them easier to tell apart.

During the 1970s two-color stroke-writing tubes were available, but not used in molecular computer graphics systems. In about 1980 made the first practical full-color vector displays for molecular graphics, typically attached to an E&S PS-300 display. This early color tube was expensive, because its was originally engineered to withstand the shaking of a flight-simulator motion base. Color raster graphics display of molecular models began around 1978 as seen in this paper by Porter on spherical shading of atomic models.

Early raster molecular graphics systems displayed static images that could take around a minute to generate. Dynamically rotating color raster molecular display phased in during 1982-1985 with the introduction of the Ikonas programmable raster display. 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 and unique, but in the 1970s the MMS-X and similar systems used (relatively) low-cost terminals, such as the series, often over 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., ) and to attach a display (such as 's MPS) directly to the. The 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 architecture. Complex graphical objects could be downloaded over a (e.g. 9600 ) 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, such as with (initially at a of 256 by 256) had started to appear. Computer-assisted in particular required raster graphics for the display of computed properties such as atomic. Although E&S had a high-end range of raster graphics (primarily aimed at the 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, coupled with the development of (e.g., and ) 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'. were often used as control devices.

Were developed based on 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 polarization for separate eyes. With projectors such as, 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.

Pymol Molecular Graphics System .psw In Powerpoint For Mac 2016

IrisGL evolved to so that molecular graphics can be run on any machine. In 1992, Roger Sayle released his program into the public domain. RasMol contained a very high-performance molecular that ran on Unix/, and Sayle later ported this to the and platforms. The Richardsons developed and the Mage software, which was also multi-platform. By specifying the chemical, 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, 's crystallography department used this to run 'Principles of Protein Structure', the first multimedia course on the Internet, which reached 100 to 200 scientists.

System

A molecule of shown without (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 programs such as and have very wide use and acceptance. Recently the wide spread diffusion of advanced, has improved the rendering capabilities of the visualization tools. The capabilities of current allow the inclusion of advanced graphic effects (like, and techniques) in the of molecules.

Pymol molecular graphics system .psw in powerpoint for mac 2016

These graphic effects, beside being, 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. Algorithms Reference frames Drawing molecules requires a transformation between molecular coordinates (usually, but not always, in units) and the screen. Because many molecules are 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.

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.