GChemPaint/C3/Features-of-GChem3D/English-timed
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Revision as of 10:53, 11 February 2015 by Sandhya.np14 (Talk | contribs)
Title of the tutorial: Features of GChem3D
Author: Madhuri Ganapathi
Key words: Menubar, File types, Model types, Change Background color, Video tutorial
| Time | Narration |
| 00:01 | Hello everyone. Welcome to this tutorial on Features of GChem3D. |
| 00:07 | In this tutorial, we will learn about: |
| 00:10 | * Menu bar |
| 00:11 | * File type formats |
| 00:13 | * Various Model types and |
| 00:15 | How to Change background color. |
| 00:18 | For this tutorial, I am using Ubuntu Linux OS version 12.04, |
| 00:24 | GChemPaint version 0.12.10, |
| 00:29 | GChem3D version 0.12.10. |
| 00:34 | To follow this tutorial you should be familiar with GChemPaint . |
| 00:38 | If not, for relevant tutorials, please visit our website. |
| 00:44 | I have opened a new GChemPaint window. |
| 00:47 | Using Templates drop down, |
| 00:49 | I will load the structure of Adenosine onto the Display area. |
| 00:53 | To save the file, click on Save icon on the tool bar. |
| 00:58 | Save as dialog box opens. |
| 01:02 | To view the file in GChem3D, it has to be saved in file formats like .mol, .mdl and .pdb. |
| 01:11 | Type the file name as Adenosine.pdb. |
| 01:15 | Click Desktop to save the file on Desktop. |
| 01:18 | Click on Save button. |
| 01:21 | I will close the GChemPaint window. |
| 01:25 | Let's now learn about GChem3D application. |
| 01:29 | GChem3D can be installed as a utility software of GChemPaint, |
| 01:34 | using Synaptic Package Manager. |
| 01:38 | Go to Synaptic Package Manager. |
| 01:40 | In the Quick filter box, type gchempaint. |
| 01:44 | Install gcu-plugin, libgcu-dbg and gcu-bin for complete installation of GChemPaint utilities. |
| 01:55 | I had already installed all the files. |
| 01:59 | GChem3d is a 3 dimensional molecular structure visualizer. |
| 02:04 | It is a utility feature of GChemPaint. |
| 02:07 | Structures drawn in GChemPaint can be viewed in GChem3D. |
| 02:12 | To open GChem3D, click on Dash Home. |
| 02:15 | In the search bar that appears, type gchem3d. |
| 02:20 | Click on Molecules viewer icon. |
| 02:24 | GChem3d Viewer window contains Menubar and Display area. |
| 02:30 | Menubar contains all the commands you need to work with GChem3D. |
| 02:36 | Display area shows the contents of an opened file. |
| 02:40 | To open a file, select File. Click on Open. |
| 02:46 | Open dialog box opens. |
| 02:49 | Select the file that you want to open. |
| 02:52 | I will select Adenosine.pdb on my Desktop. |
| 02:57 | Now click on Open button. |
| 02:59 | File is displayed on the Display area. |
| 03:02 | Let's learn to save the view as an image. |
| 03:05 | Click on File. Navigate to Save As Image. |
| 03:10 | Save as image dialog box opens. |
| 03:12 | Notice Width and Height parameters at the bottom. |
| 03:17 | Default image size has Width '300 pixels' and Height '300 pixels'. |
| 03:24 | You can increase or decrease the values using the scrollers. |
| 03:29 | Now to File type option. |
| 03:31 | GChem3D supports various file formats. |
| 03:35 | File types like VRML, PDF, PNG and others are available in the drop-down list. |
| 03:45 | If no file type is specified, GChem3d tries to determine file type from the file name. |
| 03:52 | If it does not succeed, the default File type VRML will be used. |
| 03:58 | Let's save the structure in VRML file format. |
| 04:03 | Select the option VRML document. |
| 04:07 | Type the file name as Adenosine. |
| 04:11 | Click on Desktop to save the file on Desktop. |
| 04:14 | Click on Save button. |
| 04:17 | Now we will learn what exactly is VRML File type. |
| 04:22 | VRML is a text file format with .wrl extension. |
| 04:28 | 3D polygon properties like 'vertices', 'edges', 'surface color' can be specified. |
| 04:35 | VRML files are in plain text that compress as gzip. |
| 04:40 | 3D modeling programs save objects and scenes in it. |
| 04:45 | Let us open the saved file. |
| 04:48 | Right click on the file Adenosine.wrl. Choose option Open with Text Editor. |
| 04:55 | Text editor shows all the details about the structure. |
| 05:01 | Now let us move on to Page Setup. |
| 05:04 | GChem3d uses 300 dpi resolution while printing. |
| 05:09 | Page Setup properties are the same as in GChemPaint. |
| 05:14 | I had already discussed in the GChemPaint tutorials in this series. |
| 05:19 | I will close the window. |
| 05:21 | Now let's move on to View menu. |
| 05:25 | Select View menu. |
| 05:27 | GChem3D displays a molecule using four model types: |
| 05:32 | * Balls and sticks * Space filling |
| 05:35 | * Cylinders and * Wireframe. |
| 05:39 | Balls and sticks is the default model. |
| 05:42 | Multiple bond and correct bond positions can be viewed using this model. |
| 05:48 | I will click on Space Filling and you can see the difference. |
| 05:53 | Space Filling model shows the molecules in compact form. |
| 05:58 | Cylinders model shows the structure in the form of 'cylindrical pipes'. |
| 06:03 | Wireframe model shows the 'skeletal' structure. |
| 06:08 | Let's switch back to Balls and sticks. |
| 06:11 | Now we move on to Background color. |
| 06:14 | Default background color is “black”. |
| 06:17 | Select View menu, navigate to Background color. |
| 06:21 | A sub-menu opens. |
| 06:23 | Select Custom color at the end of sub-menu. |
| 06:26 | Background color' window opens. |
| 06:30 | This window has various fields to choose the color we want. |
| 06:35 | Using Hue, we can change the background color. |
| 06:39 | Click on the scroller. Notice the change in value and movement of the color circle. |
| 06:45 | Using Saturation, we can change the concentration of the color. |
| 06:51 | Using Value, we can change the RGB combination to get different shades of the same color. |
| 06:59 | Here is the Preview box with an eyedropper icon next to it. |
| 07:04 | Click on the eyedropper icon. |
| 07:07 | Click anywhere on the color ring to choose the preferred color. |
| 07:11 | Click on OK button. Background color changes on the screen. |
| 07:18 | Let's summarize what we have learnt. |
| 07:20 | In this tutorial we have learnt about, |
| 07:23 | * Different Menus |
| 07:24 | * File type formats |
| 07:26 | * Model types and * How to Change background color. |
| 07:30 | Here is an assignment: |
| 07:33 | 1. Load a Saccharide from the GChemPaint and save the file in .mdl format. |
| 07:39 | 2. Open the structure in Molecules viewer. |
| 07:42 | 3. Save image in PNG and PDF file types. |
| 07:46 | 4. Try various background colors. |
| 07:49 | Watch the video available at this URL.http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial |
| 07:53 | It summarizes the Spoken Tutorial project. |
| 07:56 | If you do not have good bandwidth, you can download and watch it. |
| 08:01 | The Spoken Tutorial Project Team: Conducts workshops using spoken tutorials. |
| 08:06 | Gives certificates to those who pass an on-line test. |
| 08:10 | For more details, please write to contact@spoken-tutorial.org |
| 08:17 | Spoken Tutorial Project is a part of the Talk to a Teacher project. |
| 08:22 | It is supported by the National Mission on Education through ICT, MHRD, Government of India. |
| 08:29 | More information on this Mission is available at this link. |
| 08:35 | This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining. |
