Seventh European Crystaii~grap~i~ Meeting p 234 (1982) 2 Jones, A in Sayre, D ted) Crysta~i~gra~hic computing Oxford Press.

Oxford (1982) pp 303317

17 ‘A technique for the display of molecular structure diagrams on inexpensive hardware’ Rayner, J D, Milward, S and Kirby, G H Department of Computer Studies, University of Hull, Hull HU6 7RX, UK

Conventional computer display systems for molecular structures include two quite different groups. Firstly there are systems requiring high resolution graphics hardware, which use geometric information such as atom coordinates or bond lengths and angles to produce scaled projections. Secondly, there are systems which pay little attention to scale and use ordinary alphanumeric display and printing devices, providing relatively rapid output for diagrams of lower aesthetic quality.

We have developed techniques for the production of molecular structure diagrams, which are similar in style to those commonly found in textbooks and journals of organic chemistry. These line-segment diagrams come closer to the traditional unscaled sketch diagram than do alphanumeric diagrams, and yet no specialist hardware is required. Our diagrams are built up from a set of specially defined line-segment characters, which are fitted together on the row and column matrix of the typical alphanumeric display. A relatively small number of these characters is sufficient for the representation of rings, chains and unsaturations in many combinations, with ordinary letter and digit characters being used for atoms and groups. The special characters are easily implemented by extending the nortnal character set of typical microcomputers and they may be readily created by software for dot-matrix and daisy wheel printers. This technique can also be implemented by appropriate software on conventional high-resolution devices. The same diagrams can therefore be output on a variety of computer equipment.

The inexpensive nature of the hardware for which this scheme was developed permits its adoption for a wide variety of applications involving the display of molecular structure diagrams. We have investigated applications in three of these areas, namely chemical information systems, the word processing of chemical information, and education.

First, these diagrams allow output from personal, corporate or international chemical information systems to be presented in a form readily understood by the chemist, using hardware likely to be available in both the laboratory and the office. Second, technical reports prepared using word processing systems may have such structure diagrams interleaved with the text. The diagrams can be displayed and manipulated on screen in the same manner as the text, and finally printed with the text in a single operation. Third, in both secondary and tertiary education, inexpensive hardware may be used more effectively for familiarization, drill and practice in the recognition of chemical structures.

18 ‘Ellipsoidal representation of protein topography’ Taylor, W R Birkbeck College, Malet St, London, UK

A program is described which represents the shape of

globular proteins by an ellipsoidal surface. The surface is calculated as that of a solid ellipsoid with moments of inertia proportional to the a-carbons of the protein. Protein backbone structures can be displayed on an Evans and Sutherland vector graphics CRT simultaneously with a net representation of the ellipsoid. By scaling the size of the ellipsoid relative to the protein structure a good approximation to the protein surface can be found. This process is facilitated by distinguishing atoms inside the ellipsoid from those outside. The structures of 33 single domain proteins were surveyed using the program and their axial ratios compared. These were found to segregate into prolate- (disc-)like and oblate- (cigar-)like shapes. This division corresponds, with few exceptions, to a classification of proteins into [$‘a and pfi structural types, with the (YCY class of proteins lying between. The analysis is being extended to multi-domain proteins.

A modified form of the program is being used to stud} the shape of enzyme active site clefts. in this form of the program an ellipsoid derived from the inertial moments of the substrate can be fitted into the active site. The fit obtained can be compared to a manually fitted general ellipsoid in terms of volume, orientation and axial ratios.

19 ‘Computer graphics analysis of protein-ligand interactions’ Tickle, I J, Borkakoti, N and Moss, D S Department of Crystallography, Birkbeck College, Malet Street, London, UK

The recognitionI interpretation and display of the atomic interactions involved in the binding of ligands to macromolecules requires the skilful use of molecular displays. Coloured space-filling diagrams enable amino- acid residues to be colour-coded according to charge, hydrophobicity or size. Ligand tnolecules may be differently colour-coded and the use of van der Waals radii in the drawing of atoms may be exploited to reveal apparent voids in the molecular structure.

I .J Tickle has written a program (coded in Fortran IV and implemented on a DEC PDP11160) which produces hardcopy space-tilling colour drawings on a TRILOG COLORPLOT printer/plotter. In order to obtain the optimum direction of view and to eliminate parts of the structure which obscure the essential features, a line drawing of the molecular structure is pre-processed on an interactive colour display (Evans & Sutherland Picture System 2) by means of the program MIDAS.

We have used these programs to display the interactions between the enzyme pancreatic ribonuclease and the substrate inhibitor 8-0x0- guanidine-2’-monophosphate.

20 ‘Trajectory representation for molecular dynamics’ Stephen Todd IBM UK Scientific Centre, Athelstan House, St Clement St, Winchester, Hampshire, UK

Molecular dynamics simulations produce a very large output. The output is usually in a form that is rather difficult to understand. We discuss in another abstract the use of interactive animation to aid understanding.

54 Journal of Molecular Graphics

We discuss here the use of still frames showing the trajectory of certain atoms. These still frames have several advantages:

l Some features are more easily seen than with animation.

* A complete time slice may be seen at a single glance. l Cheaper hardware may be used. l Results are more easily published.

The user operates in the following steps:

l Run the simulation. l Load the result of the simulation into a database. 0 Prepare the picture. l Interact with the picture.

Simulation and data loading is covered in a paper on animation (see Abstract 21).

The picture is prepared as a set of 4D graphics primitives where the fourth dimension is time (frame number). The usual way to do this is to select a portion of the molecule and a set of frames. The last frame is shown with a stick and ball representation which may be full bond, mainchain or virtual bond. The path of each atom is then shown in a contrasting colour if hardware permits.

The picture may be controlled in various ways. Conventional rotate, pan and zoom controls change the viewing transform, using conventional 3D to 2D mapping. The mapping of time onto the 2D display surface is also controlled. Thus we have a 4D to 2D mapping.

Here is a scenario of how we use the picture control when viewing the results of molecular dynamics simulations. We colour the stick picture green, and the trajectory red. We first rotate the picture to maximize the red around the area of interest. This gives us a view showing most equivalent representations to emphasize the movement of surfaces.

Displays are prepared by the user within the database. Atable withcolumns(xl,yl,zl, rl,x2, y2,z2,t2)is then converted into 4D lines, and a table with columns (x, y, z, t) into balls or other markers. A line

(Xl (0, yl (t), zl (4. 6 x2 (4, y2 (0, 22 (4, 0

is drawn between bonded atoms 1 and 2 for the main molecule picture. A line

(x(&i), y (t-i), z (t-i), t, x (t-i-I), y (t-i-l), z (t-i-1))

is drawn to show the trajectory of an atom, where x (t) represents the x coordinate of an atom at time t, and so on, and i is a frame index. These tables are generated for a particular picture using the join, project and the other relational operators.

The display mainly used for this work was the IBM 3279, operated from our software via the IBM GDDM package, and all running on an IBM 3031. This cannot perform transformation in real time, but is easy to programme and provides colour. We have also experimented with a Vector Genera1 3300. This does permit realtime view transformation. However, these are provided by special 3D transformations hardware; it has not been designed to permit 4D transformations. Programming for 4D has been tricky, and so far we have only succeeded with display lists of about 50 4D lines.

Volume 1 Number 2 June 1983

We will probably experiment with real time 3D rotation, combined with slower interaction with the time mapping.

21 ‘Interactive animation in molecular dynamics’ Todd, S and Haneef, I IBM UK Scientific Centre, Athelstan House, St Clement St, Winchester, Hampshire, UK

Molecular dynamics simulations produce very large output. The output is usually in a form that is rather difficult to understand. We have built a system to permit the output of such simulations to be viewed as an interactive animated sequence. The user prepares for the animation with the following steps:

* Run the simulation. e Load the result of the simulation into a database. 0 Prepare a set of picture frames, one per time step. l Run the interactive animation.

The simulation is run outside our system. For the experiments so far, we have taken data on APP (Avian Pancreatic PoIypeptide) from a simulation run by W van Gunsteren and I Haneef.

The total simulation ran on a set of four molecules in water solvent, and was run for 12 ps in 240 steps.

The database used in our system is the Peterlee Relational Test Vehicle (see Abstract 13). Simulation output data is converted to a fixed file form, with data in orthogonal coordinates. To reduce the amount of data in our first experiments, we extracted only 30 frames, every third frame from the first 90 frames. Further, we did not load the hydrogen atoms and water molecules. The fixed files are loaded into the database by a standard database utility.

The data is prepared for display using the facilities of the system. These include the ability to select portions of the molecule, to highlight or label particular features and to generate bond, mainchain or backbone representations. We intend to add surface representation soon.

The preparation of each frame for an animation is exactly the same as for fixed pictures, so any feature added for fixed pictures is available for animation. For example, we are able to animate distance matrices (see Abstract 12). We hope to prepare special code for the production of a sequence of frames that takes advantage of the similarity of frames. This will reduce the current frame generation time of around 30 s/frame by at least a factor of 10. Prepared frames are saved on disc.

The animation is run specifying a first and last frame number. When the sequence is complete, animation may be stopped, or the sequence automatically rerun, of rerun in reverse. The user has interactive control over the running animation in several ways.

He controls the angle of view of the animation by a tiller (3D joystick). He controls the scale and panning from a tablet. (Not operational at 14 January 1983.) He controls the speed and direction from the terminal function keys, in one of two ways. o He may change the step used in the loop

controlling frame display. This controls direction

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