raster graphics — moleculer graphics society meeting

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Raster Graphics - Molecular Graphics Society meeting A one-day meeting on raster graphics was held at the Royal In- stitution, Albermarle Street, Lon- don, on 7 December 1982. The meeting was attended by 78 dele- gates, mostly from the UK. Dr David White (Ciba-Geigy, Basle) was the chairman for the day and there were six papers presented in four sessions. The first paper was presented by Dr Keith Prout, of the Chemical Crystallography Laboratory, Ox- ford, UK. Dr Prout began by going over the fundamentals of raster technology including the origins of the word raster. Raster comes from the Latin ‘raw-urn which means rake. The term was later used to de- scribe the five-nibbed pen used to draw staves on music manuscripts. The term was later used in architecture, then television tech- nology and now computer graphics. Dr Prout went on to compare diffe- rent raster hardware systems cur- rently available which he classed by screen resolution. Displaying molecular surfaces The second half of Dr Prout’s paper discussed how molecules may be represented on a raster screen and the advantages and disadvantages involved therein. This was based upon his group’s experience, in par- ticular the software developed by Mr Keith Davies. Dr Prout showed many examples of the use of the Ox- ford system including work with large molecules such as prealbumin. Although the resolution of the Sig- ma 5684 was only 512 x 768 pixels, the ‘staircasing’ effect was not too intrusive. When the system was used to display molecule surfaces, over 3000 vectors were displayed. Dr Prout suggested that the eye tended to omit some of the lines, making the image acceptable. Finally, Dr Prout showed some of the recent work carried out by Mr Davies in Professor R Langridge’s laboratory in the University of Cali- fornia, San Francisco, California, USA. A film showed the use of the system on the same type of graphics terminal linked to a VAX1 l/780 by a 26 19.2 kbaud line. Animation was achieved by swapping between two pairs of bit planes. Dr Rodney Keat, Glasgow Uni- versity, UK, discussed and demons- trated his viewing system for an Ap- ple II microcomputer. Apple UK kindly loaned a microcomputer to the Royal Institution for Dr Keat’s lecture. One point of interest was to decide how much could be achieved on a system costing about $1500. System development The first step in developing this sys- tem was to survey the graphics pack- ages available. Two were considered in some detail, they were l sub Logic A2-3Dl l Bill Budge There were drawbacks to both of these packages as far as this applica- tion was concerned, mainly in either the time taken to rotate in 3D or the resolution offered. Dr Keat decided to develop his own system. It is in five parts: 0 file system l fractional to orthogonal coordin- ates transformation 0 matrix multiplication l transformation to screen coordin- ates l line plotting The file system is currently under development. The transformation between fractional and orthogonal coordinates is written in interpreted BASIC. The matrix multiplier, screen coordinates transform and the plotting routine are written in 6502 machine code. At this time, the matrix multiplier handles 3 x 3 rota- tion matrices without perspective or translation. A look-up table is used for the trigonometrical functions. The multiply operation is very im- portant in attempting to build a sys- tem capable of real-time interaction, and Dr Keat spent some time ex- plaining the different options open to him. Using the AM 9511A arith- metic processor, the time taken to calculate a floating point multiplica- tion was reduced from 3000 ps to 50 N. Dr Keat also explained the prob- lems he encountered with the plot- ting routines. In order that he could use broken lines as an intensity depth cue and so that the procedure could be speeded up, he coded Bresenham’s algorithm. The advan- tages of the new plotting routine and matrix multiplier were demons- trated using ATP (34 vectors). The system was refreshing the display 30 times per second, however, and there was a great deal of flicker on rotation of the molecule. One of Dr Keats colleagues in Glasgow, Dr Kelvin Tyler, has de- veloped a graphics processor for this work. This hardware is based upon the Thomson EFC1.5 graphics pro- cessor chip which has a resolution of 512 x 512. The processor also in- cludes separate graphics memory, a character generator and a plotting speed of 1 Mpixels/s. Using this pro- cessor, Dr Keat again demonstrated the system this time using a larger molecule (54 vectors). The trans- formation of the molecule was much faster and was only limited by the speed of the Apple matrix multi- plication. Finally vitamin B12 was put up on the system to demonstrate that larger molecules could be hand- led by the extended system. Space-filling diagrams Dr John Pearson, Roche Products, demonstrated the work he has been carrying out on a Ramtek 6211 sys- tem. This system is mainly used for taking slides of molecules and para- metric plots, and at Roche is hung on a PDP11/40. Dr Pearson began by describing the 6211. It is a system based on the 280 processor and is capable of displaying 16 colours from a palette of 64. It has its own interpreted graphics language. Dr Pearson then went on to de- scribe the problems he had encoun- tered in carrying out this work. His method of producing space-filling di- agrams of molecules is to order the atoms along the axial direction into the screen, using a bubble sort. The circumference of a circle represent- ing the outline of the first atom is drawn and then the area is filled. This is repeated for each atom suc- cessively painting over the atoms previously drawn. The polygon fill facility of the Ramtek was found to Journal of Molecular Graphics

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Page 1: Raster graphics — moleculer graphics society meeting

Raster Graphics - Molecular Graphics Society meeting A one-day meeting on raster graphics was held at the Royal In- stitution, Albermarle Street, Lon- don, on 7 December 1982. The meeting was attended by 78 dele- gates, mostly from the UK. Dr David White (Ciba-Geigy, Basle) was the chairman for the day and there were six papers presented in four sessions.

The first paper was presented by Dr Keith Prout, of the Chemical Crystallography Laboratory, Ox- ford, UK. Dr Prout began by going over the fundamentals of raster technology including the origins of the word raster. Raster comes from the Latin ‘raw-urn which means rake. The term was later used to de- scribe the five-nibbed pen used to draw staves on music manuscripts. The term was later used in architecture, then television tech- nology and now computer graphics. Dr Prout went on to compare diffe- rent raster hardware systems cur- rently available which he classed by screen resolution.

Displaying molecular surfaces

The second half of Dr Prout’s paper discussed how molecules may be represented on a raster screen and the advantages and disadvantages involved therein. This was based upon his group’s experience, in par- ticular the software developed by Mr Keith Davies. Dr Prout showed many examples of the use of the Ox- ford system including work with large molecules such as prealbumin. Although the resolution of the Sig- ma 5684 was only 512 x 768 pixels, the ‘staircasing’ effect was not too intrusive. When the system was used to display molecule surfaces, over 3000 vectors were displayed. Dr Prout suggested that the eye tended to omit some of the lines, making the image acceptable.

Finally, Dr Prout showed some of the recent work carried out by Mr Davies in Professor R Langridge’s laboratory in the University of Cali- fornia, San Francisco, California, USA. A film showed the use of the system on the same type of graphics terminal linked to a VAX1 l/780 by a

26

19.2 kbaud line. Animation was achieved by swapping between two pairs of bit planes.

Dr Rodney Keat, Glasgow Uni- versity, UK, discussed and demons- trated his viewing system for an Ap- ple II microcomputer. Apple UK kindly loaned a microcomputer to the Royal Institution for Dr Keat’s lecture. One point of interest was to decide how much could be achieved on a system costing about $1500.

System development The first step in developing this sys- tem was to survey the graphics pack- ages available. Two were considered in some detail, they were

l sub Logic A2-3Dl l Bill Budge

There were drawbacks to both of these packages as far as this applica- tion was concerned, mainly in either the time taken to rotate in 3D or the resolution offered. Dr Keat decided to develop his own system. It is in five parts:

0 file system l fractional to orthogonal coordin-

ates transformation 0 matrix multiplication l transformation to screen coordin-

ates l line plotting The file system is currently under development. The transformation between fractional and orthogonal coordinates is written in interpreted BASIC. The matrix multiplier, screen coordinates transform and the plotting routine are written in 6502 machine code. At this time, the matrix multiplier handles 3 x 3 rota- tion matrices without perspective or translation. A look-up table is used for the trigonometrical functions. The multiply operation is very im- portant in attempting to build a sys- tem capable of real-time interaction, and Dr Keat spent some time ex- plaining the different options open to him. Using the AM 9511A arith- metic processor, the time taken to calculate a floating point multiplica- tion was reduced from 3000 ps to 50

N. Dr Keat also explained the prob-

lems he encountered with the plot- ting routines. In order that he could

use broken lines as an intensity depth cue and so that the procedure could be speeded up, he coded Bresenham’s algorithm. The advan- tages of the new plotting routine and matrix multiplier were demons- trated using ATP (34 vectors). The system was refreshing the display 30 times per second, however, and there was a great deal of flicker on rotation of the molecule.

One of Dr Keats colleagues in Glasgow, Dr Kelvin Tyler, has de- veloped a graphics processor for this work. This hardware is based upon the Thomson EFC1.5 graphics pro- cessor chip which has a resolution of 512 x 512. The processor also in- cludes separate graphics memory, a character generator and a plotting speed of 1 Mpixels/s. Using this pro- cessor, Dr Keat again demonstrated the system this time using a larger molecule (54 vectors). The trans- formation of the molecule was much faster and was only limited by the speed of the Apple matrix multi- plication. Finally vitamin B12 was put up on the system to demonstrate that larger molecules could be hand- led by the extended system.

Space-filling diagrams Dr John Pearson, Roche Products, demonstrated the work he has been carrying out on a Ramtek 6211 sys- tem. This system is mainly used for taking slides of molecules and para- metric plots, and at Roche is hung on a PDP11/40. Dr Pearson began by describing the 6211. It is a system based on the 280 processor and is capable of displaying 16 colours from a palette of 64. It has its own interpreted graphics language.

Dr Pearson then went on to de- scribe the problems he had encoun- tered in carrying out this work. His method of producing space-filling di- agrams of molecules is to order the atoms along the axial direction into the screen, using a bubble sort. The circumference of a circle represent- ing the outline of the first atom is drawn and then the area is filled. This is repeated for each atom suc- cessively painting over the atoms previously drawn. The polygon fill facility of the Ramtek was found to

Journal of Molecular Graphics

Page 2: Raster graphics — moleculer graphics society meeting

create problems where atoms over- lapped. This was overcome using the box facility. Each atom was repre- sented by filling 127 pixels.

Elastase was shown as an example of a protein being displayed on this system and the result was good, although the speed of drawing the picture was quite slow. The inter- calation of daunomycin into DNA was shown as an example of the use of selective colour coding to empha- size specific features.

Dr Pearson also discussed the use of half-tone shading by filling alter- nate pixels and the problems caused by interlacing the display with this shading. Taking slices through the molecule also caused problems and Dr Pearson went into some detail about how these problems were overcome. The use of this low-cost terminal was seen by Dr Pearson as an ideal medium for producing high quality hardcopy.

Surface algorithms

Following lunch, Professor J Brick- man of the Technische Hochschule, Darmstadt, gave an overview of the work his group has undertaken on surface algorithms. The talk concen- trated on the realistic representation of objects composed of spheres.

Professor Brickmann began by giving a description of his raster graphics system. The system is based upon a Grinnell 512 X 512 system with &bit planes. The graphics de- vice is hung on a PDP11/60. One part of the system that has been de- veloped by the group is an editor for generating look-up tables. This in- teractive facility enabled the user to select the colour(s) required and to view the maximum number of in- tensity levels for the number of col- ours chosen. Examples of the col- ours and intensities used were given. For example, for drawing energy surfaces, 32 colours are used with eight intensity levels per colour. Pro- fessor Brickmann showed how the

look-up table can be manipulated to emphasize certain features. One striking example was the identifica- tion of nucleation sites in compress- ed argon gas.

Lighting algorithms The next part of the presentation covered the algorithms for display- ing reflected light from the atoms’ surfaces. Ways of giving the effect of highlights, soft lighting and back- lighting were discussed and com- parisons made, of spheres lit in diffe- rent ways. Some examples of grama- cidin lit in different ways were also presented.

Finally, Professor Brickmann showed us some examples of his hobby, computer art. Shading algor- ithms and various look-up tables were used to produce some very startling and extremely effective pic- tures.

Dr Roderick Hubbard (see paper in this issue) described the system he has built on the Research Machine 3802 microcomputer. The total sys- tem cost $4000 about 18 months ago. The main reason for purchasing a Research Machine 3802 was that the software already existed to download data from a DEClO main- frame, which is the computer used on the York University, UK, cam- pus. Dr Hubbard described his sys- tem (this is not repeated here as it is covered by his paper) and then showed a video of the system in op- eration. In fact, Dr Hubbard was one of the first researchers to use video for showing his system in op- eration and this medium is now be- coming very popular at conferences. The examples given by Dr Hubbard were species of insulin and hemoglo- bin which are currently being in- vestigated by the Chemistry Depart- ment of the University of York. Arguably, the most exciting part of Dr Hubbard’s work is his imagina- tive mixture of graphics and image.

The final speaker was Professor Arthur Lesk from Fairleigh Dickin-

son University, New Jersey, USA, who is currently on sabbatical at the Laboratory of Molecular Biology, MRC Laboratory, Cambridge, UK. Professor Lesk talked about the general use of graphics tools for the molecular biologist and stressed the need for flexibility, abstract repre- sentation and colour. His own graphics work started with a prog- ram that drew ribbon and cylinder representations of proteins’ secon- dary structures on a line plotter. Va- rious features of this program were found to be of most value when com- bined with other types of repre- sentation. So the program de- veloped so that it could handle hid- den line removal or leave the cylin- ders and sheets translucent, and so that line and space-filling repre- sentations could be added to the dis- play to accentuate certain features. One feature that was found to be of great value was the ability to select part of the picture to be zoomed up.

Colour representation

Later, Professor Lesk required col- our to be able to compare different structures or produce red/green stereo. This made him think that he would really prefer a full-colour rep- resentation of the structure. Profes- sor Lesk started work on this at the IBM Thomas J Watson Research Centre, Yorktown Heights, New York, USA, with Dr Karl Hardman. The program is still being de- veloped, but Professor Lesk showed some examples of his latest work. The ribbons and cylinders are col- oured and shaded giving a realistic representation of the schematic view (this does sound like a contradic- tion). Professor Lesk finally gave ex- amples of how the use of colour sim- plified complicated structures.

Dr White closed the meeting by thanking all those who had taken part and the members of the group who had helped to organize the day. Andrew J Morffew

Volume 1 Number 1 March 1983 27