Graphics programs md publications

Mel, G and Sussman, J L 7LORTEP: a computer program b translate PLUTO instructions hto those of ORTEP’ J Appl. crytdogr. Vol 16 pp 650-651

PLORTEP is a small Pascal ~ngmm that takes input in the style $ PLUTO and translates it for ORTEP. In this way the best @ures of both plotting programs in be combined_ The authors &nd this necessary because ‘&tahographers prefer the thermal dlipsoids of ORTEP. So far this &rogram has run under two IBM operating systems, TSO and VM.

!I&, P A, Pattabiraman, N, Exang, C, Ferrin, T E and WaSe, R ‘Van der Waals &aces in molecular modelling: inpIementation with reai-time ajmputer graphics’ Science Vol222 !#a 4630 pp 1325-1327

MIDAS now indudes a new surface perator which ailows rotation about bonds, while maintaining a Cuaprehensible dot surface. This @&XI uses a bit lattice, similar to that nsed by Pearl and Honegger, to -&ntify interior atoms. Some -pies of the use_ of the new .dgorithm are given. The cover we shows a view of B DNA baking down the axis and a view of t6c rose window from Washington cathedral. Both display tenfold rlmmetry.

ba, J aud Schubert, W ‘Computer whng of molecular structures’ ~pu&a&Chem. Vol7No2

Ii& paper describes a program c&d MAGIC which is used to enter F .Organic compounds and edit -g ones. The interaction is by %htpen and the graphics terminals c the GT40 and VTlOO. There is Ibo a version which uses a Tektronix Q4 storage tube.

Bus&a, B, Tickle, I J and BlandelI, T L ‘DOCKER, an interactive program for simulating protein receptor and substrate interactions’ J. Appl. Crystallogr. Vol 16 pp 432-437

One of the programs to be developed in the Department of Crystallography, Birkbeck College, UK. It uses the Pearl and Honnegger algorithm for producing dot surfaces which is coupled with a molecular mechanics program. The substrate is flexible and can be fitted to the active site by energy minimization or manual interaction. The BELL facility warns the user when disaBowed.contacts occur. The program is written in Fortran IV and runs on an Evans and Sutherland Picture System 2.

COMOUY, M L ‘Analytical molecular surface calculation’ J APPL Clystaiogr. Vol 16 pp 548-558

This paper describes Connolly’s new aigorithm in some detail. The output consists of a set of curved regions of spheres and tori, joined together at circular arcs. The paper includes all equations and details required to understand this method. It is an interesting and well-written paper.

Connolly, M L ‘Solvent-accessible surfaces of proteins and nucleic acids Science VolZ21 No 4612 pp 709-713

At last, the latest work from the inventor of dot molecular surface representations for vector refresh displays. Now he has turned his attention to raster graphics and therefore to an analytical form of the surface. This paper descriis the analytical molecular surface and shows examples on raster and vector colour terminals. The pictures are very good and, in particular, the solvent accessible raster representa- tion appears to be very informative.

Deken, J Computer images: state of the art Thames and Hudson (1983)

Published both in hard and soft covers this small coffee-table style book has over 250 superb dour reproductions. Just the thing to whet the appetites of new graduate students.

F&an, J T, Burt, S K and MacElroy, R D ‘Viewing the energy optimiza- tion of chemical models with com- puter animation’ Comput. Chem. Vol7 No 4 pp 165-173

This paper describes the use of an animation system to play back the optimization of chemical models. Frames’ are kept on disc and then transferred to a minicomputer buffer memory. From here they are fed to the graphics device refresh buffer. Using an Evans and Sutherland stroke device, the update rate can be 18 frames/s. With a Terak raster device, this rate falls to l-2 frames/s. Frames can be accessed randomly as weil as in sequence, allowing pairs of frames to be superimposed.

Henry, D R ‘Modifications to program Spacetil to produce shaded space-f?lling molecular models with perspective’ Comput. Chem. Vol 7 No 3 pp 119-135

As the title states, this paper describes two modifications to Spacefil. First, a perspective transformation is included. Second, shading is applied to all atoms. Previously the shading option was only used for hetero atoms. The appendix includes details of the changes that need to be made to the code, together with a full listing of the new program.

Hout,RFPietro,WJandHehre,W J ‘Orbital photography’ J. Comput. them. Vol4 No 2 pp 276-282

This paper describes a program for producing images of molecular orbitals on 1024 x 1024 raster terminals. The methods used are z- buffering and the Cook-Torrance shading modei. The paper gives good

explanations of these methods and some examples of the images produced. Unfommateiy, coolour was not available for the authors. The authors also mention that they use half-toning so that pictures may be produced on a Vematec plotter; no details are given of this algorithm.

h4arsii, M, -Fioersheim, P and Dreading A S ‘Generation and comparison of space-filling molecular models’ Cornput. Chem. Vol 7 No 4 pp 175-181

This group appears independently to have invented the Pearl and Honegger algorithm for rapid generation of molecular surfaces (J. Mol. Graphics Vol 1 No 1 pp 9-12). Here it is applied to small molecules_ Some other features of the program are described and the authors show that thii program could be of value in a drug design system. The system is based on a PDPlll attached to a GT41 graphics terminal.

Miller, K J, Kowalczyk, P, SegmnIler, W and WaIker, G ‘Interactions of molecules with nucleic acids. VII. Evaluation and presentation of steric contours and molecules in binding sites’ 1.

CompuLar. Chem. Vol 4 No 3 pp 366378

This paper describes a method of displaying electrostatic contours and molecules to investigate docking, in this case intercalation of small molecules with DNA. The contours are displayed as a stack of planes, with hidden-line removal for chiri.fication. An example of one of these pictures is given in Max’s review (see p 8). In this paper the method of producing these pictures is described .and some examples of use are given.

pickover, C A ‘Spectrographic representation of globular protein breathing motions’ Science Vol 223 No 4632 pp 181-182

Clifford Pickover spetialises in applying graphical representations from different branches of science to molecular biology. In this paper he describes the use of spectrograms and power spectra in the analysis of molecular dynamics data. These representations are familiar in some other branches of science, for example, speech analysis. Pickover uses these representations to identify the

lower-frequency modes of the vibration of BFTI. He compares his method with some other techniques.

Tucker, J B “Designing molecules by computer’ High Technology (January 1984)

There have been many reviews on the use of computers in drug design in the popular scientific press. This review is one of the better attempts and iS even readable and informative for those working in this area. The picture are good and the author has taken the trouble to research the field thoroughly.

Zientara, G P and Nagy, J A ‘Proteins and poiypeptides - computer graphics for space-filliig mode! representations’ Cornput. aid Chem. Vol 7 No 2 pp 67-74

A plotting program for polypeptides which accepts input in Brookhaven format. It includes the facility for partitioning the molecules according to some predefined categories, such as residue names and charge group

types.

Graham R&&r&

22 fournat of 3loIecutar Graphics