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------------------------------------------------------------ The Arachne Molecular Modeller - Demonstration Version by David Miller and Jim Cameron Copyright © Arachne Software 1993 ------------------------------------------------------------ HENSA Distribution Demonstration Manual --------------------------------------- Copyright © Arachne Software 1993 All rights reserved This demonstration version of the Molecular Modeller may be freely copied and distributed providing the complete set of files including all documentation files is copied and is not altered in any way whatsoever. No part of this package may be distributed on its own or incorporated in any other software package or other product. A charge may not be made for this software other than distribution/media costs. Any attempt to disassemble, reverse assemble, reverse compile or interpret this software is illegal, and Arachne Software reserve the right to prosecute any person found to be attempting this, or to be including any part of this software in programs developed or used by themselves. While every care is taken, Arachne Software cannot be held responsible for any errors in this product, or for any consequential loss or damage from the use of this product, even if Arachne Software have been notified in advance of any such possible loss or damage. The Arachne Molecular Modeller was written by David Miller & Jim Cameron. This demonstration was prepared for distribution by Tim Barrett. Published by Arachne Software Orchard Cottage, East Morden, Wareham, Dorset, BH20 7DL System Resources ================ The modeller makes use of various standard system resources. Before it is loaded an up to date !System directory must have been 'seen' by the filer, as must a !Fonts directory containing the Trinity.Medium font. Introduction ============ The Application Icon -------------------- When the modeller has loaded it will place its green application icon towards the right of the icon bar. Clicking Menu over this opens the Modeller menu. Moving over the arrow to the right of Info displays a dialogue box giving information about the version of the modeller you are using. Please quote this version number in all correspondence with Arachne about the modeller. Choosing Quit removes the modeller from the desktop. The Molecule Display Window --------------------------- Clicking Select over the icon bar modeller icon opens the molecule display window. The central green area contains any loaded molecules or fragments. The two yellow rotation bars allow the molecule to be quickly rotated to any orientation. Displaying Molecules ==================== Loading ------- First you will need a molecule to display. Several examples are included for you to experiment with. Double-clicking on a molecule will load it. Load in Methane as an example. You should be presented with the Molecule display window. Rotating the Molecule --------------------- The display can be rotated by dragging or clicking in one of the two yellow rotation bars at the bottom and right of the central green area where the molecule itself is displayed. Try it. Moving the Molecule ------------------- If you move the pointer over the central green area and have not experimented with too many other areas of the modeller, it should turn into a hand. Dragging the mouse pushes the molecule around the window. Not all of the molecule need be on the window all the time – if it is pushed off the edge it is only lost from view, not from memory. The Rendition Control Window ---------------------------- With the Molecule display window open, type Ctrl-R. The Rendition control window will be opened. PLOTTING STYLE This is used to choose how molecules are displayed. The 'dragging plotting style' is used when rapid update of the display is required, for example when rotation bars are being dragged or the display is being pushed around with the hand. The normal plotting style is used at other times. To change a plotting style, click on the grey arrow to the right of it then choose a style from the resultant menu. BONDS ONLY displays a line between each pair of bonded atoms and as such is quick and ideal for a dragging style. BALL AND STICK considers each atom of a solid sphere, the size of which is related to the size of the atom. Bonds are drawn between the spheres as lines. QUICK FILL draws an atom as a sphere, providing only elementary hidden surface removal. Bonds are not drawn. SPACE FILL is similar to quick fill but provides rigorous hidden surface removal and as such takes considerably longer. Outlined space fills (see Plotting Options below) use a more precise (but slower) technique. SYMBOL STRUCTURE is recommended for output to a desktop publishing package for monochrome printing. It is similar to ball and stick except that the atoms are represented by their symbols. STEREO LINE is a version of bonds only for use with red and green 3D glasses. The red goes over the left eye, and the green over the right eye. The principle of stereoscopy - fooling the brain into thinking it is seeing in three dimensions - is used. It is most effective when used in calculated animations with molecules which have closed loops in them, such as Naphthalene. If you do not have any 3D glasses, they can be obtained by sending £1 to Arachne. See the file, 'order'. The full modeller comes with 3D glasses. Try changing the normal plotting style. If you have not already done so, open the Rendition control window with Ctrl-R. Click on the arrow to the right of the normal plotting style and choose Space fill from the Style menu. Click on OK at the bottom right of the widow to confirm you choice. (In line with standard RISC OS practice, if you click select, the window closes automatically, whereas adjust leaves it open for further changes to be made.) PLOTTING OPTIONS This section of the window is used to enhance the display to make it clearer or make the two-dimensional screen display look less flat. Outline atoms produces, where appropriate, an outline around each atom to help separate it from its neighbours. Perspective makes atoms at the back smaller than those nearest to you. The colours menu allows atoms to be shaded so that the further back an atom is, the darker it becomes. The shaded option works best in 256 colour modes, while the dither options only work in 16 colour modes, and will not print out. Spacefill atom dither gives spacefilled atoms an enhanced spherical appearance. Try changing the plotting options. Choose Spacefill atom dither. Remember to click on OK to confirm your choice. Also make sure that you are in a 16 colour mode such as 12, 20 or 27 (or if you must stay in a 256 colour mode choose Shaded black to back). The third section controls the angle through which the molecule is rotated as it is displayed. The X and Y axes are in the plane of the screen. Click on the arrows at either side of each angle or click on the angle and edit it to change the angle. (Rotation is usually performed more easily by dragging the rotation bars in the display window.) The view size section is used to zoom in on a molecule. To select a preset size click on its yellow icon. Alternatively click over the current size and edit it or click on the increase/decrease arrows at either side. There are three buttons at the bottom of the rendition control window. OK, as you have already seen, is used to confirm any changes made to the rendition settings and update the display accordingly. Cancel does the opposite. None of the changes are applied and the rendition control is reset to its previous state. Clicking on Save is equivalent to clicking on OK, except that it also stores the current settings as the defaults used next time the modeller is loaded. Remember, clicking on any three of these buttons with adjust leaves the rendition control window open, while select closes it – just like a menu. When a molecule is saved, all rendition control details are saved with it so that when it is loaded it will be displayed in the previously chosen way. This allows optimum initial rotation settings and rendition types to be saved. The Display Submenu ------------------- Pressing menu over the molecule display window gives the main modeller menu. One submenu from this is the display submenu. The first four options simply open their respective windows. The rendition control window has already been mentioned – the others will be dealt with later. Resizing the Display Window --------------------------- If the display window is resized some or all of the rotation bars may be cut off. Next in the Display submenu is Resize. Choosing this updates the display window so that the rotation bars are visible. Choosing Autosize causes a resizing operation to be performed every time the window's size is changed. Full Screen Display ------------------- Although described in the chapter on molecular animation, the Full screen display choice can be used at any time. Choosing it will probably rotate the display in the centre of the screen until the mouse is clicked again. Animation Creation ================== In order to help visualise a molecule it is often useful to make it rotate on its own. There are several ways to do this, so that you can select the best for your machine's capabilities and for your own taste. Calculated Animations --------------------- The simplest animations to use are calculated animations – in which the molecule is drawn as fast as possible in slightly different positions. Load up a fairly small molecule such as Methane then choose MiniAnim from the Animate submenu. The Mini-animation control window will be opened and, assuming not all of the rotation steps are 0°, the molecule will start to rotate. The three editable numbers in the Mini-animation control window are the angles of rotation between successive displays in the X, Y and Z directions respectively. To cancel the mini-animation close the Mini-animation control window. Full Screen Calculated Animations --------------------------------- Slightly faster and smoother results can be achieved with calculated animations if they take over the whole screen rather than running in a window. Choosing Full screen from the display window shows a calculated animation, with angle steps the same as those last set up in the Mini-animation control window, on the whole screen. When using the Stereo Line display style, moving the mouse towards you or away from you moves the molecule correspondingly. Click the mouse to exit from the full screen animation. Recorded Animations ------------------- Recorded animations can not be used with the demonstration modeller. They are described here for interest only. Although calculated animations may well be adequate for small molecules, particularly on machines with ARM 3 processors, higher speeds are sometimes required. In such cases it is necessary to pre-calculate and record each frame of the animation. This has the disadvantage of limiting the maximum number of frames to the available memory but it does mean that large molecules can be animated effectively. Choosing Recorded from the Animate submenu opens the Recorded animation setup window. Two types of recorded animation are supported : rotation about an axis and animation about an arbitrary line. Recorded Animation about an Axis -------------------------------- Select the top section of the window by clicking select on the radio button to the left of Rotate about axis. Click select on the axis about which you wish to rotate and enter the required angle step between each frame. The smaller the step the smoother the animation, but more frames are required so more memory will be used. More Interesting Recorded Animations ------------------------------------ Select the lower section of the window by clicking select on the radio button to the left of Rotate about arbitrary line. The X, Y and Z axis steps are identical to those in the Mini-animation window. However, particular care should be taken to ensure that over the number of frames requested the molecule is rotated a complete number of turns (an integer multiple of 360°) in each direction so that the end of an animation joins up correctly with its start. The number of frames can be set to any value up to 360 but as always, the more frames you use, the more memory you will need. Designing & Editing =================== The Tools Window ---------------- Designing and Editing are done almost entirely with the aid of the toolbox, a small window which positions itself at the left of the display window. To open the toolbox, type Ctrl-T or choose Tools from the Display submenu. At the top of the toolbox the current tool is named, 'Move Display' in this case. Below this is the selected button. This is used with many tools to make them operate on the currently selected atoms, as opposed to a single atom or all the atoms. The majority of the toolbox is taken up with a 3 by 3 grid of nine tools. The currently selected one is highlighted in orange. A tool in the grid is chosen by clicking select. Clicking adjust on many of the tools opens a subsidiary window related to the tool in question. For example, clicking adjust over the Add atom tool opens the Periodic table window. In the descriptions below you will come across tools which do not appear in your toolbox. There are more than nine tools available but rather than having a larger toolbox containing a confusing profusion of tools, you can select the tools you use the most frequently and position them where you find logical. By clicking menu over a tool, its space in the grid can be reallocated to another. Try clicking menu over the tool at the top left of the toolbox and try choosing one of the tools in the resultant menu. Shaded tools can not be chosen because they are already in the toolbox. The bottom of the toolbox is used for displaying occasional messages or giving information about the state of the currently active tool. Select ------ This tool is used in conjunction with the 'selected' button and the Select submenu to change the effect many other tools. Just as in a word processing package you can cut and paste selected text, in the modeller you can cut and paste selected atoms. Many tools will only affect selected atoms if the 'selected' button is highlighted. Click adjust over the 'select' tool to choose whether you wish to select single atoms or entire fragments. (A fragment is a group of atoms which are bonded together.) Click over an atom to select an atom or fragment. Clicking select clears any previous selection first, while adjust adds to it, in the same way as in a directory window. Choosing All from the Select submenu selects every atom in the display. Choosing Clear deselects all the atoms. Move Display ------------ Dragging the 'move display' hand over the display window moves all structures around. Pushing things off the edge only loses them from view – it does not remove them from memory. Zoom ---- The magnifying-glass tool can be used to zoom in and out the display. Clicking Select over the display reduces its size and Adjust increases it. Add Atom -------- Clicking select over the display adds an atom of the currently chosen element in the plane of the screen. Elements are chosen from the Periodic table window, opened by clicking adjust over the 'add atom' tool or by pressing Ctrl-E. An element is chosen by clicking over it, or by typing its symbol into the Periodic table window and pressing Return. Remove Atom ----------- Clicking on an atom removes it from the display. If 'selected' is highlighted and remove atom clicked, or 'selected' is clicked when 'remove atom' is the current tool, all selected atoms are removed. Bond Atoms ---------- Clicking on two atoms bonds them together. Clicking adjust over the tool opens a window from which single, double, triple or aromatic bonds can be chosen. A bond's type can be changed by re-bonding with the new type. Bonds are only displayed in 'bonds only', 'ball and stick' and 'symbol structure' rendition types. Remove Bond ----------- Clicking on two atoms removes the bond between them. Bonds are only displayed in 'bonds only', 'ball and stick' and 'symbol structure' rendition types. Translate --------- Dragging over the display moves the atom nearest to the pointer around the display, or all selected atoms if 'selected' is highlighted. Unlike 'move display', which simply changes the displayed position of all the structures, 'translate' works on an individual atom or selected atoms. Clicking adjust over the tool opens a window allowing the axes of the dragging to be chosen. Normally atoms are dragged in the plane of the screen, but if 'Drag in X and Z planes' is selected moving the mouse up and down moves atoms away from or towards you. (Effectively pushing the mouse away from you pushes atoms away from you and vice versa.) Select Centre ------------- All atoms in the display window rotate about the same fixed point. It is often desirable for a structure to rotate about a particular atom and this is achieved by translating the structure so that this atom is at the centre of rotation. Clicking on an atom makes rotation take place around it. If 'selected' is highlighted only the selected atoms will be translated. Rotate Bond ----------- 'Rotate bond' can be used to manually correct a bond angle. Click first on the central atom, then on an atom in the group joined to the central atom which you wish to rotate. The arrows at the bottom of the extended toolbox can then be used to rotate about the central atom. Atom Info --------- 'Atom Info' displays the atom type currently pointed to at the bottom of the toolbox. It also shows the number of the atom in order of creation. Check Length ------------ 'Check length' is used for measuring the distance between two (usually bonded) atoms. Click on each atom in turn and the distance between them is shown at the bottom of the toolbox. Check Angle ----------- 'Check angle' measures the bond angle between two atoms bonded to a central atom. Click on one outside atom, the central atom and then on the other outside atom, and the angle between them is shown at the bottom of the toolbox in degrees and minutes. Background Structure Prediction =============================== The Setup Options window ------------------------ The Setup options window is used to select the required background structure prediction. Bond-length Correction ---------------------- The modeller knows the average bond lengths of the most common bonds including those found in the A-level Chemistry Data Book by J. Stark & H. Wallace. When it finds a bond of unknown length it uses an estimated length from the radii of the two atoms. Background Operation -------------------- To try to ensure that you are not interrupted there is a short delay after you do something before background operation starts. Also, to ensure that the rest of the desktop is not slowed up, molecular modeller background operations only occur when the pointer is over the display window. Please note that background operations may not function if the !Help interactive help application is loaded. This is not the case with the full version of the Modeller. When molecules are loaded, background structure prediction is turned off. Since these operations cause molecules to be redisplayed continuously, complex displays might slow down the computer if background operations were left enabled.