****************************************************************** Molecule 3D is a Public Domain Share-ware release from West Germany. You are welcome to copy this program and distribute it as long as it is not sold and this documentation remains with it. The author is: Rainer Paape Paschenburgstr. 67 2800 Bremen 1 West Germany (The newest update may be purchased from him) The documentation was imported and translated by: Robert Zimmerer 131 W 2nd Street Port Angeles, WA 98362 (206) 452-7529 If you are interested in more software from germany and for details about this and other progrrams, feel free to call or write me. *See adendum for more info. ****************************************************************** Molecule 3D Info You must have the following files in a folder named MOLEKUEL on your disk in order for the program to work: - MOLEKUEL.PRG (contains the program) - MOLEKUEL.DAT (contains the program logo) - RADIEN.DAT (contains Atom-, Ion- and v.d. Waals-Radii) - FARBEN.DAT (contains graphics for color coordination) - RGB.DAT (contains data for color coordination) The following files are also useful: - DEMO.KOO (Demo-file for coordinates) - DEMO.BIN (include file of bonds for DEMO.KOO) - DEMOx.PI2 (Demo graphics for high resolution) - DEMOx.PI1 (Demo graphics for medium resolution) - TEST.KOO (Demo-file for positions of axi in space) - TEST.BIN (include file of bonds for TEST.KOO) - Molecule.DOC (This file in 1st-Word format) - Molecule.TXT (This file in ASCII) General notes: Two sets of information are necessary for molecule representation. - Atom symbols and X,Y and Z-coordinates - Binding list of the atoms Up to 216 atomic coordinates and 216 bonds can be defined. The maximum number of pictures in a sequence depends on the amount of free memory. The program determines the maximum number of pictures allowed, each requiring about 19 Kbytes of RAM. Around 40 pictures can be made using a 1040ST (or 520ST with 1Megabyte of RAM) having with TOS in ROM. After about 30 pictures the going gets pretty slow. The program operates in high and medium resolution! Starting the program: Once you are in the Molcule folder, double-klick on "MOLEKUEL.PRG" to start the program. If the necessary files are not in order an error message will appear and you will be returned to the desktop. If all goes well, you will be given a menu. The bottom of the screen displays memory and data information as well as the free space on the disk in the drive. The drive shown is the default drive, from which the program was initiated. If you want to change drive specifications (to a second disk drive, a RAM disk or Hard disk), click on the right or left arrow until you are at the drive. To check how much free space you have on the selected drive, click on the "Freier Speicher" box (to the left of the drive selection box) 1 Data ( Daten ) 1.1 Editing the coordinates ( Koordinaten editieren ) In order to edit the coordinate values of the molecule, pull down the menu item labeled "Daten" and click on the "KOORDINATEN EDITIEREN" entery. This takes you to an editor displaying the data entries in a ledger format. Once in the editor, you may edit any column by clicking on the entry. The key will take you to the next line of the column and write the new information to that line of the column. When you are finished entering data in the column, press the key. (Be sure to press to write the information before pressing ) To move through the list, click on the arrow symbols at the top of the screen. The single arrows move the list one entry in either direction, the double arrows move it 15. The column labeled "Art" is for the atomic symbol, and the coordinates of the molecule go in the X, Y and Z columns. In the line marked "Molekl" you may enter the name of the molecule. Clicking on the box marked "Menue" returns you to the main menue. 1.2 Editing bonds( Bindungen editieren ) Here you may enter/change the bonds list. Entering and editing the data follows the same rules in with the coordinate editing section. After entering the atom pairs, the type of bond will be shown (eg. C-C). The bond lengths are also calculated and displayed. This allows you to check the accuracy of your entries and find bonds that are to short or long. The program also checks if the atoms are available. If, for example, 37 atomic coordinates were defined and a bond between atoms 34 and 38 were entered, a bond between "34 + 0" would be displayed. It is therefore important to enter or load the atomic coordinates. 1.3 Saving coordinates/bonds ( Koordinaten/Bindungen speichern ) When you are finished entering the data you should always save it right away. Click on the boxes marked "KOORDINATEN SPEICHERN" and "BINDUNGEN SPEICHERN" to save coordinates and bonds respectively. The extensions should be ".KOO" for coordinate data and ".BIN" for bonding data. (from the german KOOrdinaten and BINdungen) 1.4 Loading coordinates/bonds ( Koordinaten/Bindungen laden ) In order to load a Coordinate or Bonds file, click on the entries "KOORDINATEN LADEN" for coordinate data and "BINDUNGEN LADEN" for bonds in the "Daten" drop down menu. 1.5 Deleting Coordinate/Bonding ( Koordinaten/Bindungen l”schen ) When you click on the entries "KoordinatenL”schen" or "BindungenL”schen", all the data is erased from memory. 1.6 Merging Coordinates/Bonds ( Koordinaten/Bindungen mischen ) This menu entry allows for the union of two or more data groups. For example, if you wanted to compare two molecules together on the same screen you would: first load in the coordinate data of the first molecule followed by its bonding data. Next merge the coordinate data of the second molecule with the menu entry "Koordinaten mischen". Follow this by merging the bonding data of the second molecule with the menu entry "Bindungen mischen". You may merge as many molecules as you want, so long as there is enough space in the memory. (see above for maximum values) It is very important that you are careful to follow this procedure exactly, always alternate between loading coordinates and bonds! 1.7 Editing Radii( Radien editieren ) To get into the radius editor, click on the menu entry maked "Radien Editieren". (See above for editor controls) The elemental symbol "CA" stands for carbon in aromatic orbits, and "CM" stands for carbon in methylene groups. This distinction is only meaningful in the van der Waals- radius. All the radii are given in units of the coordinate system (Angstoms). 1.8 Saving Radii ( Radien speichern ) To save radius data, the diskette in the default drive must contain the folder "MOLEKUEL" since the data is always saved to the file "RADIEN.DAT" in the folder "MOLEKUEL". If the folder is not found, error # -34 (pathname not found) occurs. This data is automatically loaded at the beginning by the program since all th necessary information for the diagram of the radii is contained in it. Great care should be taken to ensure that this data is not lost! 2. Importing data ( Inport ) Since the atomic coordinates come originally from a mini computer, you should try to port coordinate data from a mini computer through the RS-232 port if the opportunity shoild present itself. This will save you the time consuming and "typo"-full task of entering all the data by hand. Data entry routines will be released for normal calculations. 2.1 Loading MNDO-Data ( MNDO-Daten laden ) If you want to load atomic coordinate data from an MNDO list (MNDO-Rechnung), the data must have the following structure: Row 1 Column 1-80: Molcule's name (comments) Row 2-n Symbol and coordinates of the atom, with the following requirements: Columns 16-17: atomic symbol or number upto 20 Columns 21-30: X-coordinates Columns 31-40: Y-coordinates Columns 41-50: Z-coordinates Row n+1 Columns 1-2: /* Row n+2 Columns 1-2: // The format of rows 2 to n are in the form of the output from the "MOPAC" program in version 2.00. Rows 1, n+1 and n+2 must be filled out by hand prior to loading. 2.2 Loading "Ab-Initio-Daten" ( Ab-Initio-Daten laden ) This feature hasn't been implemented yet! 2.3 Loading "Gauss80-Daten" ( Gauss80-Daten laden ) This feature hasn't been implemented either! 3 Graphics ( Grafik ) 3.1 View ( Zeigen ) Shows the last calculated or loaded graphic. 3.2 Inverting ( Invertieren ) Shows the last calculated or last loaded graphic in inverted form. 3.3 Hardcopy Prints a copy of the last shown graphic. The operating systems printing routine is used for this. If your printer isn't supported, you must first load the appropriate printer driver for your machine. The hardcopy can be printed then through the screen dump command ( ). 3.4 Loading ( Laden ) Loads a previously saved graphic. 3.5 Saving ( Speichern ) This saves the last calculated and shown graphic as an entire screen. In monochrome the pictures have the extension ".PI2" and can be loaded into and modified by graphics programs that handle monochrome. When saved from a color monitor system, the color information isn't saved. You can use "PAINTER.ST" to modify these pictures. 4 Colors ( Farben ) This menu selection can only be selected from medium resolution. 4.1 Setting RGB values ( RGB-Werte einstellen ) This menu selection allows you to adjust the settings of the red, green and blue for the display. By wearing a pair of red/green glasses and loading the file called "FARBEN.DAT", you can get the real "3D" effect. 4.2 Loading/Saving Color settings ( RGB-Werte laden/speichern ) With these menu selections (RGB-Werte laden/RGB-Werte Speichern), the color settings can be loaded and saved. 5 Graphics Calculations ( Menue_2 / Grafik Berechnen ) Here you get a new drop down menu which allows all the parameters for the representation of the molecule to be laid out and adjusted. This menu will only be selectable after coordinates and bonds are available (having been entered or loaded). This screen contains a window (2/3 the screen) for displaying the molecule, and a group of parameter control boxes on the right. 5.1 Modes ( Modi ) 5.1.1 Rotation around Original/Actual Axis ( Rotation um Ursprungs/aktuelle Achse ) When rotating around the original axis, the molecule is turned around the X, Y or Z axis. These axii are horizontal and verticle from the observer's perspective. When rotating around the actual axis, the chosen spin is taken into consideration for the X and Y axii respectively. (se below for details) The default is rotation about the original axis. 5.1.2 Rotation around the X, Y or Z axis ( Rotation um die X, Y oder Z-Achse ) Determines which of the three axii the rotation will be around. The default is the X axis. 5.1.3 Projection ( Projektion ) With verticle (senkrechter) projection the molecule is represented without distortions. Perspective (perspektivischer) projection distorts objects which are closer in the view more than the objects which are further away. The default is "senkrechte" projection. 5.2 Graphics ( Grafik ) 5.2.1 Radii ( Radien ) Determines if and which radius should be at the end of bond (only in "senkrechter" projection). If the radii (Radien) is selected, the "BINDUNGEN ZEICHNEN" should first be deselected. The default setting for radii is no radius (kein Radius). 5.2.2 Atom symbols ( Atomsymbol ) Determines if the atom symbol will be displayed. (this feature only works in "senkrechter" projection and only when the radii are not selected!) The default is no atom symbols (kein Atomsymbol). 5.2.3 Atomic number( Atomnummer ) This displays the atomic number of the atom (same restrictions as with atomic symbols). The default is no atomic number (keine Atomnummer). 5.2.4 Show Axis ( Achsen zeichnen ) Determines if the axii of the coordinate system will be displayed or not. The default is no axis (nicht einzeichnen). 5.2.5 Show bonds ( Bindungen zeichnen ) Determines if the bonds will be displayed or not. The default is show bonds (einzeichnen). 5.3 Pictures ( Bilder ) 5.3.1 Single/Animate ( Einzelbild/Bildfolge ) When single picture (Einzelbild) is selected, only one molecule is displayed. When Animate (Bildfolge) is selected, the molecule is rotated around the axis selected in Mode (Modus). The default is single (Einzelbild). 5.3.2 Picture size ( Bildgr”že ) When 1/1 is selected, the entire display window is used for the molecule diagram. When 4/4 is selected, the window is divided into quarters, each showing a different view of the molecule. The default is 1/1. 5.3.3 Color Stereo Picture ( Farbiges Stereobild ) This feature may only be selected in medium resolution. Two pictures are drawn (detailed in 5.5.7) which differ by a specified angle. With the help of Red/Green glasses you can get an appearence of space (see 4.1). This only works in 1/1 picture setting. 5.4 Measure ( Mažstab ) Determines whether the size of the diagram is automatically or manually set. Default is automatic. 5.5 Setting the numerical Parameters Setting the numerical parameters is done by clicking on the left or right arrow associated with the parameter. Clicking the right mouse button will increase or decrease the value by ten, the left button will change the value by one. Holding either button down will cause the value to change until the button is released. 5.5.1 Pictures ( Bilder ) This is the number of pictures used in an animation sequence. The maximum value depends on the amount of free memory. The number of pictures is inversely proportional to the rotation angle. The default is the maximum. 5.5.2 Rotation angle( Drehwinkel ) Shows the angle of rotation between pictures in an animation. The minimum value depends on the amount of free memory. The angle is closely related to the number of pictures in the animation. The default is the smallest angle possible for the amount of free memory. 5.5.3 X/Y Rotation ( Drehung um X/Y ) Determines how many degrees the molecule will be rotated in space. The default is 0 in each case. 5.5.4 Size in Pixels( Gr”že in Pixeln ) Determines the half size of the graphic in pixels. Also works when the measure is automatically calculated. The default is 150. 5.5.5 Distance ( Abstand ) Determines the distance the observer is from the object (only in perspective projection). The default value is 16. 5.5.6 Unity ( Einheit ) Determines how many pixels a unity in the coordinate system. A change in this value only has an effect when the setting for the Measure is in manual. the default value is 40. 5.5.7 Stereo picture difference ( Stereobild Differenz ) Determines how many degrees the stereo pictures are seperated from one another. The setting is in tenths of degrees. The default value is 2.5 degrees. 5.5.8 Show Picture ( Zeige Bild ) Displays the pictures in the animation on the entire screen as long as an animation has been calculated. 5.5.9 Speed ( Geschwindigkeit ) Adjusts the speed with which the molecule rotates in an animation. 5.5.10 Start Begins the calculation of a molecule or shows a prepared animation. All of the previous functions like calculating and drawing may be canceled by pressing the right mouse button. 5.5.10 To Menu ( Zum Menue ) Returns you to the main menu. Subject to change w/o notice ----------------------------------------------------------------- * Translater's Adendum: I must apologize for any inaccuracies in relation to chemical terminology. I have had the usual High School chemistry courses and found some of the german terms identifiable. I cannot be held responsible for any possible damage or defamation of character that might be incured upon use of this software. As stated above, this is Public Domain Share-ware from West Germany, and may contain references to programs and software not available in the USA. This translation of the documentation is also released into the Public Domain with the only restrictions being that it may not be sold. Copy it and pass it on. I have organized a disk which includes: a copy of the original software package, including german documentation, my most recent translation and a handy translation sheet to help you in operating the program and reading the menus. If you would like the disk & translations, send $5.50 (to cover disk, shipping & handling, import costs & translating) to: Robert Zimmerer Disk order 131 W 2nd Street Port Angeles, WA 98362 For more information about other PD software from West Germany you may write to the above address or call at: (206) 452-7529