GChemPaint/C3/Features-of-GChem3D/English-timed

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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.

http://spoken-tutorial.org/NMEICT-Intro]

08:35 This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14