..................... i~l~ : ~ : ~ . - rCOMPUT~R CORNER RASMOL: biomoIecular graphics for all Recent advances in crystallography have led to an almost explosive increase in the number of macromolec- ular structures that have been solved at atomic resolution. Transcription fac- tors, protein-nucleic.acid complexes, actin and myosin, signalling proteins, translation factors, photosynthetic complexes and the energy-generating F:-ATPase (to name only a few) are all Figure :1, Nuclear magnetic resonance structure s of an even- numbered, zinc-finger DNA.blndlng domain, a frag- ment of the human male-associated protein ZFY (PDB code 5ZNF). It shows an a-carbon plot (in BACKBONE mode) of the main chain, colour coded by sequence. The amino terminus is blue and the carboxyl termi- nus red. The zinc atom is at the centre and the two cysteine and two histidine ligands are shown in atomic detail. Also visible are the main-chain-main-chain hydrogen bonds, drawn between the a-carbon atoms, confirming that the secondary structure consists of an a-helix and a I~hairpin. revealing secrets of their construction and, in many cases, the secrets of how they work. However, seeing these interesting molecules for yourself can be a prob- lem. First, you need the coordinates, which are often slow to appear in the public domain, and second, you need access to powerful computers dedicated to molecular graphics. Although the first problem remains, the second is becoming less acute, thanks to the in- creasing power of desktop computers and the avail- ability of programs for them. Tools are now available that allow a wider public to view zmd manipulate mol- ecules in va:~ous ways, overcoming the difficulty of representing three dimen- sions on screens or printed pages. This article focuses widely available of these programs, RASMOL. A number of design features make RASMOL easy to use, even for begin- nets. It is available free of charge from a variety of file- transfer protocol gtp) sites (for example, by anonymous ftp from ftp.dcs.ed.ac.uk). It loads structures quickly and directly from standard Brookhaven Protein Data Bank (PDB) files and runs TmBS 20 - SEPTEMBER 1995 on almost all current computers, in- cluding Unix workstations, personal computers running Windows, and Macintoshes. Indeed, the three-dimen- sional rotation of space-filling models can be faster on a Power Macintosh than some of the professional programs running on top-of-the-line graphics work-stations. Several different repre- sentat|ons are available, including wire- frame, spacefiU, a-carbon backbone, strands, ribbons and, soon, Richardson- style cartoons (Figs 1, 2); and the inter- conversion between different views is fast. Ligands, active sites, multiple sub- units, hydrogen bonds and various parts of the molecule can Jso be dis- played selectively or in a combination of display modes. It is easy to colour atoms, residues or subunits to your per- sonal choice, which is a powerful aid to understanding the relationship be- tween structure and function, or that between primary, secondary and tero tiary structure. Once an image has been created, it can be printed directly or translated into a variety of formats for display or alteration by other graphics programs. Full use of the display features in RASMOL requires both correct use of the mouse and knowledge of typed commands. The latter have deliberately not been added as menu items so that the set of menus presented to the first- time user is simple. However, it is easy to use RASMOL (as E. J. M-W. did ini- tially) without finding out the commands needed for the different display tools or knowing how to use the mouse properly for three-dimensional manipula- tions. RASMOL has a user manual, but, like many user manuals, it is easier to use when you know what you're looking for. Table I and Box 1 summarize the facilities offered and explalr, how to realize the full potential of the program quickly. Table I. Three.dimensional manipulation in RASMOL Macintoshes PCs (IBM compatible) and Unix/XWindows Rotate molecule about any axis in the x,y plane Drag cursor in the appropriate direction Drag cursor in the appropriate direction using the left mouse button Zoom molecule Translate moleculewithin x,y plane Rotate molecule about the z-axis a Drag cursor vertically with the shift key pressed Drag cursor with the command key pressed Move cursor with both the shift and command keys pressed Drag cursor vertically using the left mouse button and with the shift key pressed Drag cursor using the right mouse button Drag cursor using the right mouse button and with the shift key pressed aTo ensure the point of rotation is the midpoint of the whole molecule (the default), type centre. To allow rotation about a particular residue, say number 30, type centre30. 374 © 1995, Elsevier ScienceLtd 0968-0004/951509.50