Revised February 2004 36H Molecular Modeling Tutorial Using MacSpartan Pro and or PC Spartan Pro Adapted by K Milks PSU 02 from the original by L Schmiedekamp PSU 99 Adapted from the work of Ted West and Mark Lanasa Penn State University And from the work of Dr Richard Smith Western Maryland College Don t bother to read this tutorial ahead of time Work through it while sitting at the PCSpartan or MacSpartan workstations in Room 207 Whitmore Bring a highlighter or colored pen to emphasize parts of the tutorial you find useful this will help you when you need to do the modeling component of your project Working through the tutorial in pairs may be beneficial One person can read the instruction steps aloud while the other uses the software Take turns reading and computing Make sure to complete the two page worksheet at the end of these instructions each person must turn in a worksheet Getting Started When you sit down to a MacSpartan Pro workstation if the monitor is dark first hit the space bar to see if it is the screensaver If that does not work for one of the PowerMacs then push the restart button in the upper right hand corner of the keyboard with the arrow and wait for the user login screen When you sit down to the PC Spartan Pro workstation you should see a window that flashes around the screen which says Press Ctl Alt Delete to log on If the screen is black hit the space bar to turn it on Hints for Macintosh computers The menu bar across the top of the screen varies depending on the active program or represents the functions of the Finder if no programs are active In order to use a pull down menu use the mouse to position the cursor on top of the desired item in the menu bar press but do not release the mouse button slide the cursor down to the desired sub menu item and release the mouse button The Apple Menu far left of the menu bar will vary depending on the active program The Apple Menu while MacSpartan is the active program is useful for information about MacSpartan for changing the colors within MacSpartan please change back to the default when you are finished and for other MacSpartan preferences The far right icon on the menu bar will show the icon of the active program or a little computer face if the Finder is active To switch between opened programs click and hold on the far right icon and drag down to highlight the program you wish to use If the program has a window opened you can also click on that window to make that program active You can have several programs open at once but only one can be active Hints for Windows 2000 Drop down menus require one click and they stay opend until the menu item is selected or you click again on the menu heading Any program window can be closed by clicking on the X button at the upper right hand side The button at the upper right with the hyphen will minimize the program onto the TaskBar The button at the right with the two rectangles will change the size of the window or maximize it You can switch between opened programs using the icons on the TaskBar next to the Start button 1 MacSpartan Workstation If no one has logged on type or choose crc as your name the password is also crc lowercase Once the Mac desktop appears double click on the MacSpartan Pro icon located on the desktop Go to the File menu and select New you ll automatically be in the Builder Mode of Spartan Under the File menu click Save The Save window will appear choose New Folder give the new folder your name then click Create Note 1 If you are doing the tutorial with a partner you can share a folder for the tutorial but you will need separate folders for all of your project data Close the window by clicking Cancel 2 PC Spartan Workstation Press the Ctrl Alt and Delete the delete button is near the number pad buttons simultaneously and then click OK in the first window to bring up the login screen Login as crc lowercase the password is also crc lowercase Click on the PCSpartan Pro icon locatd on the desktop Go to the File menu and click New you are now in the Builder Mode of Spartan Under the File menu choose Save In the Save As window click on the Create New Folder icon a yellow folder with a Name the folder as your name hit the Enter key and close the window Note If you are doing the tutorial with a partner you can share a folder for the tutorial but you will need separate folders for all of your project data Building molecules To familiarize yourself with Mac PC Spartan Pro you will construct several molecules and perform some simple calculations Mac Whenever you wish to make a new molecule you use the Builder module of MacSpartan Pro You do this by selecting File then New from the pull down in the menu bar of MacSpartan Pro This moves you into the Builder module of MacSpartan Pro Here you will be able to build your molecule and name the file The Builder display is divided into two regions a work area where you construct the molecule and the Model Kit area which occupies the right third of the screen and contains a variety of molecule building editing tools Note If you ever need to edit a molecule in MacSpartan Pro select the Build menu then find Edit Structure and you will return to the builder with the molecule which was selected at the time PC Whenever you wish to make a new molecule you open the Building Mode by selecting File then New from the pull down in the menu You will notice that only one molecule can be displayed at a time when in this mode others will disappear from your view and that on the right is a model kit area with a variety of molecule building editing tools Note If you ever need to edit a molecule in PC Spartan Pro select the Build menu then Add Fragment or Delete Atom Make Bond or Break Bond and you will be able to edit the molecule which was selected at the time Now that you are in the building mode we will go over the various tools available In the model kit area there are three tabs at the top Entry Expert and Peptide You will only be using the Entry mode in this class In the Entry mode you will see a group of raised buttons bearing the symbols for a number of atoms The atomic symbols are surrounded by lines which indicate the hybridization e g sp3 sp2 or sp and valency number of possible bonds of a particular element For example in the upper left you see a C with four separate lines around it in a roughly tetrahedral …