1 00:00:01 --> 00:00:09 Hello everyone. Welcome to the tutorial on Edit Preferences, Templates and Residues in GChemPaint. 2 00:00:10 --> 00:00:12 In this tutorial, we will learn to: 3 00:00:13 --> 00:00:14 * Edit Preferences 4 00:00:15 --> 00:00:16 * Manage Templates 5 00:00:17 --> 00:00:19 * Select and use ready Templates 6 00:00:20 --> 00:00:23 * Add a New Template 7 00:00:24 --> 00:00:25 We will also learn: 8 00:00:26 --> 00:00:27 * The uses of Residues and 9 00:00:28 --> 00:00:30 * To edit Residues. 10 00:00:31 --> 00:00:37 Here I am using Ubuntu Linux OS version. 12.04, 11 00:00:38 --> 00:00:43 GChemPaint version 0.12.10. 12 00:00:44 --> 00:00:48 To follow this tutorial, you should be familiar with 13 00:00:49 --> 00:00:52 GChemPaint chemical structure editor. 14 00:00:53 --> 00:00:58 If not, for relevant tutorials, please visit our website. 15 00:00:59 --> 00:01:02 I have already opened a new GChemPaint application. 16 00:01:03 --> 00:01:06 Let's begin the tutorial by editing Preferences. 17 00:01:07 --> 00:01:12 Go to Edit menu, navigate to Preferences and click on it. 18 00:01:13 --> 00:01:15 GChemPaint Preferences window opens. 19 00:01:16 --> 00:01:23 The first field, Default Compression Level For GChemPaint Files, is used when saving files. 20 00:01:24 --> 00:01:27 By default, it is zero. 21 00:01:28 --> 00:01:32 If not zero, the file will be compressed using gzip. 22 00:01:33 --> 00:01:39 I will cover Invert wedge hashes in an another tutorial. 23 00:01:40 --> 00:01:45 In GchemPaint, each document has an associated theme. 24 00:01:46 --> 00:01:49 Let's retain the Default Theme as GChemPaint. 25 00:01:50 --> 00:01:57 Now, I will explain about Arrows in detail, under Themes section. 26 00:01:58 --> 00:02:01 Observe the different types of arrows on the tool box. 27 00:02:02 --> 00:02:05 * Add an arrow for an irreversible reaction. 28 00:02:06 --> 00:02:09 * Add a pair of arrows for a reversible reaction. 29 00:02:10 --> 00:02:13 * Add an arrow for a retrosynthesis step. 30 00:02:14 --> 00:02:18 * Add a double headed arrow to represent mesomery. 31 00:02:19 --> 00:02:23 Let's add these 4 arrows to the Display area. 32 00:02:24 --> 00:02:27 Click on Add an arrow for an irreversible reaction tool. 33 00:02:28 --> 00:02:30 Then click on Display area. 34 00:02:31 --> 00:02:40 Likewise, I will add other types of arrows to the Display area. 35 00:02:41 --> 00:02:46 Select Arrows from the Themes field in the Preferences dialog box. 36 00:02:47 --> 00:02:49 A Contextual menu opens. 37 00:02:50 --> 00:02:56 Here we can increase or decrease Length, Width and Distance of the arrows. 38 00:02:57 --> 00:03:01 Click on up or down arrow triangles with the mouse. 39 00:03:02 --> 00:03:09 And Observe the changes in the arrows in the Display area. 40 00:03:10 --> 00:03:13 Now let's learn about Arrow heads. 41 00:03:14 --> 00:03:20 The default values of A, B and C are displayed here. 42 00:03:21 --> 00:03:27 The A, B and C parameters help to vary the shape of the arrow heads. 43 00:03:28 --> 00:03:37 Increase or decrease each one and observe the changes in the arrow heads. 44 00:03:38 --> 00:03:41 Let's click on Close button, to close the window. 45 00:03:42 --> 00:03:45 Let's clear the Display area. 46 00:03:46 --> 00:03:48 Press Ctrl +A to select all objects. 47 00:03:49 --> 00:03:52 Go to Edit menu, click on Clear. 48 00:03:53 --> 00:03:57 Next, let's learn how to manage Templates. 49 00:03:58 --> 00:04:00 Click on Use or manage templates tool. 50 00:04:01 --> 00:04:04 The property dialog box opens below. 51 00:04:05 --> 00:04:09 Property dialog box contains Templates with a drop down list. 52 00:04:10 --> 00:04:18 List contains Amino acids, Aromatic hydrocarbons, Nucleic bases, Nucleosides and Saccharides. 53 00:04:19 --> 00:04:22 Each item has a Submenu. 54 00:04:23 --> 00:04:30 Let's select Aromatic Hydrocarbons and click on Benzene from the Submenu. 55 00:04:31 --> 00:04:34 Benzene structure is displayed on the property page. 56 00:04:35 --> 00:04:39 Now click on the Display area to display Benzene structure. 57 00:04:40 --> 00:04:48 Likewise let's select Naphtalene structure and click on the Display area. 58 00:04:49 --> 00:04:54 Select and place other structures on the Display area, on your own. 59 00:04:55 --> 00:04:56 Let's save the file now. 60 00:04:57 --> 00:05:00 Click on Save the current file icon on the toolbar. 61 00:05:01 --> 00:05:03 Save as dialog box opens. 62 00:05:04 --> 00:05:09 Enter the file name as Benzene. Click on Save button. 63 00:05:10 --> 00:05:15 Now let's learn to add a New template to the existing Template list. 64 00:05:16 --> 00:05:19 Click on Open a file icon from the toolbar. 65 00:05:20 --> 00:05:23 A window with files and folders opens. 66 00:05:24 --> 00:05:26 Select the file named “Hexane” from the list. 67 00:05:27 --> 00:05:30 Click on Open button. 68 00:05:31 --> 00:05:34 Click on Add button from the template's property page. 69 00:05:35 --> 00:05:37 New template property page opens. 70 00:05:38 --> 00:05:41 Property page has two fields – Name and Category. 71 00:05:42 --> 00:05:46 Category field has a drop down list. 72 00:05:47 --> 00:05:51 We can select from the list or add our own category. 73 00:05:52 --> 00:05:57 Let's add a new Category, by typing Hydrocarbons in the text field. 74 00:05:58 --> 00:06:02 In the Name field, enter the name of the compound as “Hexane”. 75 00:06:03 --> 00:06:06 Click on the Hexane structure on the Display area. 76 00:06:07 --> 00:06:11 It will be displayed on the New template property page. 77 00:06:12 --> 00:06:14 Click on OK button. 78 00:06:15 --> 00:06:18 Now, click on Templates drop-down. 79 00:06:19 --> 00:06:21 Select Hydrocarbons category. 80 00:06:22 --> 00:06:26 Observe that Hexane structure is added to the Template list. 81 00:06:27 --> 00:06:31 Add Octane structure to Hydrocarbons category, on your own. 82 00:06:32 --> 00:06:34 Let's close the “hexane” file. 83 00:06:35 --> 00:06:40 Go to File menu, select Close to close the file. 84 00:06:41 --> 00:06:46 Click on Select one or more objects tool to close the Templates property page. 85 00:06:47 --> 00:06:50 Now, let's learn about Residues. 86 00:06:51 --> 00:06:52 Residues are used to, 87 00:06:53 --> 00:06:57 * Find the nature of functional group attached to carbon chain. 88 00:06:58 --> 00:07:00 * Know the structure of functional group. 89 00:07:01 --> 00:07:03 * Add a new functional group to the database. 90 00:07:04 --> 00:07:08 Go to Tools menu, click on Edit residues. 91 00:07:09 --> 00:07:11 Residues window opens. 92 00:07:12 --> 00:07:17 It has three buttons - New, Save and Delete. 93 00:07:18 --> 00:07:20 New button has a drop down list. 94 00:07:21 --> 00:07:24 Select n-Pr for from the list. 95 00:07:25 --> 00:07:31 Identity tab shows Symbol and Name of the selected residue. 96 00:07:32 --> 00:07:37 Formula tab shows the Skeletal structure of the selected residue. 97 00:07:38 --> 00:07:43 Likewise, let's select s-Bu for Secondary Butyl. 98 00:07:44 --> 00:07:51 Observe the Symbol, Name and Skeletal structure of the selected residue. 99 00:07:52 --> 00:07:56 Let's now add a new residue - Hydroxy group. 100 00:07:57 --> 00:08:01 To add a new residue, click on New button. 101 00:08:02 --> 00:08:05 In the Symbol field type O-H. 102 00:08:06 --> 00:08:08 Name it as Hydroxy. 103 00:08:09 --> 00:08:10 Click on the Formula tab. 104 00:08:11 --> 00:08:13 You will see a bulleted bond. 105 00:08:14 --> 00:08:18 Place the cursor near the bond and press capital O. 106 00:08:19 --> 00:08:23 A Submenu opens with O and Os. Select 'O'. 107 00:08:24 --> 00:08:27 O-H group attaches to the bond. 108 00:08:28 --> 00:08:30 Click on Save button. 109 00:08:31 --> 00:08:34 Now, click on New button to view the list. 110 00:08:35 --> 00:08:39 Observe that O-H residue is added to the list. 111 00:08:40 --> 00:08:43 Let's click on Close button to close the window. 112 00:08:44 --> 00:08:47 With this we come to the end of this tutorial. 113 00:08:48 --> 00:08:49 Let's summarize. 114 00:08:50 --> 00:08:52 In this tutorial, we have learnt to: 115 00:08:53 --> 00:08:54 * Edit Preferences 116 00:08:55 --> 00:08:55 * Manage Templates 117 00:08:56 --> 00:08:58 * Select and use ready Templates 118 00:08:59 --> 00:09:00 * Add a New Template 119 00:09:01 --> 00:09:06 * Uses of Residues and To edit Residues. 120 00:09:07 --> 00:09:11 As an assignment: * Select and use Saccharides from Templates list. 121 00:09:12 --> 00:09:15 * Explore other residues. 122 00:09:16 --> 00:09:19 Watch the video available at this URL. http://spoken-tutorial.org/What_is_a_Spoken_Tutorial 123 00:09:20 --> 00:09:23 It summarizes the Spoken Tutorial project. 124 00:09:24 --> 00:09:28 If you do not have good bandwidth, you can download and watch it. 125 00:09:29 --> 00:09:32 The Spoken Tutorial Project Team: Conducts workshops using spoken tutorials. 126 00:09:33 --> 00:09:36 Gives certificates to those who pass an online test. 127 00:09:37 --> 00:09:44 For more details, please write to contact@spoken-tutorial.org. 128 00:09:45 --> 00:09:49 Spoken Tutorial Project is a part of the Talk to a Teacher project. 129 00:09:50 --> 00:09:56 It is supported by the National Mission on Education through ICT, MHRD, Government of India. 130 00:09:57 --> 00:10:03 More information on this Mission is available at this link [http://spoken-tutorial.org/NMEICT-Intro ] 131 00:10:04 --> 00:10:09 This is Madhuri Ganpathi from IIT Bombay signing off. Thank you for joining.