OVERVIEW ======== DRAWNA is a program devoted to fast rendering of 3-D lighted, solid models of nucleic acids. It allows the user to choose between several kinds of representation (wire, CPK, balls & sticks, ribbons & rods) through a Motif control panel. Drawna reads standard *.pdb files, and may associate to each coordinate file one or several H-bond file (*.hbd) or parameter file (*.prm). These files are automatically generated through transient windows. DRAWNA demands IRIX 4.0.5 or higher, and at least a 8-biplanes framebuffer and a 16-bitplanes depthbuffer. We recommend however to use it on a Extreme workstation, including a 1280*1024 display with a full 24-bitplanes framebuffer and a dial box. This program was developped by Christian Massire in the Equipe de Modelisation et Simulation des Acides Nucleiques - UPR 9002 CNRS - Institut de Biologie Moleculaire et Cellulaire 15 rue Rene Descartes 67084 STRASBOURG cedex FRANCE reference : DRAWNA : A Program for drawing schematic views of nucleic acids C. Massire, C. Gaspin, E. Westhof J. Mol. Graphics, (1994), 12, 201-206 E-mail : massire@royo.u-strasbg.fr THE MAIN COMMAND WINDOW ======================= This window contains the following widgets : Push Buttons : -------------- - Redraw : used to activate redrawing after changing a viewing parameter. - Picture Mode : redraws the entire scene within a full-screen borderless window. the Esc key is used to exit. Radio Buttons : --------------- - wire : the covalently linked atoms are connected by straight lines; - CPK : each atom is represented by its Van der Waals volume; - flat : flat ribbon for sugar-phosphate backbones and rods for H-bonded pairs; - conic : high-quality ribbons and rods with possibly Ball & Stick models Toggle Buttons : ---------------- - Auto Redraw : when set, enables dispatching of redrawing events. You may have to disable it in order to avoid useless redraws while handling windows. - Double buffer : swaps between single buffer and double buffer mode. Double buffer is useful while displaying wire models, since their high-speed drawing allows real-time handling. - Filled : displays Ribbons, rods and spheres using a lighted, Gouraud-shaded tesselation or only the outline patches. - Two-toned : indicates whether or not ribbons are drawn using two different colors for the front and back sides. Also indicates if rods are drawn accordingly to the ribbon color or to their base color. - Stereo : when set, the 3D window is divided into 2 viewports, each one showing the same scene, but viewed from a slightly different point of view. Each viewport is always centered on its focus point, so the stereo gap is changed while resizing the 3D window. The angle between both lines of sight is defined by a scale widget in the parameters window. Positive values indicate direct stereo view, while negative ones indicate reverse stereo view. - Fog : enables or disables atmospheric effects. Each pixel color is blended to the background colour, according to its Z-buffer value. Fog starts at the z = + slab/2 plane and becomes completely opaque at the z = - slab/2 plane. - Base Pairs : in ribbon views, shows all paired bases as rods. (see Pair Editor) - Free bases : in ribbon views, shows all bases but paired ones as rods pointing from the ribbon to the N1 or N9 atom of the base. - Spheres : display spheres on specified phosphorous atoms (see Sphere Editor) Scale Widgets : --------------- - Rx, Ry, Rz : rotation angles (in degrees) the centre of rotation is by default the coordinates origin, and is afterwards moved to any atom picked with the middle mouse button. - Tx, Ty, Tz : translations values (in Angstroms) for the centre of rotation. - Zoom : uses a logarithmic scale. - Slab : indicates the depth of the viewing volume. The dial box may be used in wire mode with the following usage : Zoom | Slab --------|-------- Rz | Tz --------|-------- Ry | Ty --------|-------- Rx | Tx THE MENU & THE TRANSIENT WINDOWS ================================ File View Lighting Help Open File... Background Color Ribbons About DRAWNA... Read Parameters Bases List Atoms & Bases Num Pad shortcuts... Save Parameters Fragment Editor Light Source Quit Pair Editor B & S Editor Parameters... Open File... Calls the default file selection dialog. The H-bond file name and parameters file name are automatically updated while selecting a coordinate file. It is however possible to select other files. Background Color Select either a black, white, or RGB background. The RGB color is defined by the three neighbouring scale widgets. Bases List : This window consists in two lists, showing the nucleotides names in the order 5' -> 3' and 3' -> 5'. Both lists are used to select bases in the following editors. Fragment editor : This window consists in three parts : the first one lists strands as they are recognized while reading the coordinate file. This strand partition into strands can not be changed. However, it is possible to add extra strand fragmentation, by clicking the Add button and selecting the base starting the new strand from one of the bases list. The two other parts are used to specify the ribbon width and thickness, as well as the ribbon color for the current fragment (see the Ribbons Color Editor). The drawing toggle button allows the selection of the displayed fragments. Pair editor : This window list the currently defined rods. To Add a pair, click the Add Button and select the desired bases in the bases lists. To remove a pair, click the Remove Button and then the pair in the neighbouring list. Sphere Editor : This window is used to add spheres on ribbon control points coordinates (by default Phosphorous atoms). B & S Editor : The Ball & Stick Editor allows to emphasize particular bases by displaying them with an atomic resolution in one of the ribbon drawing mode. They may be colored accordingly to the atom-coding or to the base-coding color table (see Atoms & Bases Window) or with the neighbouring ribbon color. Parameters : The drawing step and sphere depth scale widgets indicate how accurate are drawn ribbons and sphere respectively. The fitting Coordinates Toggle Button forces the ribbon to pass through control points, making the ribbon less smooth but more accurate in highly-curved regions. The stereo distortion scale indicates in degrees the deviation of the line of sight for both stereo viewports. Ribbons Color Editor : 8 couples of front- and back-color are available for drawing ribbons. Each color is defined by 3 sets of parameters : - DIFFUSE : components R,G and B of the light which is uniformly reflected in all directions. They define dull materials. - SPECULAR : components R,G and B of the light which is reflected perpendicular to the ribbon. They define bright materials. - SHININESS : when null, disables the SPECULAR reflection. Otherwise, larger values spread specular reflectance. Atoms & Bases Color Editor : works the same way as above, but is applied to colour definitions used for Ball and Stick models. Light source : allows to define the R,G and B components of the light source, as well as its location. When the POINT LIGHT SOURCE toggle is set, the sliders x,y and z indicate the position of a point light source, otherwise it is located infinitely far beyond this point.