Difference between revisions of "GChemPaint/C3/Features-of-GChem3D/English-timed"

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Title of the tutorial: '''Features of GChem3D'''
 
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Author: '''Madhuri Ganapathi'''
 
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Key words: '''Menubar,  File types,  Model types,  Change Background color,  Video tutorial'''
 
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{|border=1
 
{|border=1
 
|'''Time'''
 
|'''Time'''
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|00:01
 
|00:01
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|Hello everyone.Welcome to this tutorial on '''Features of GChem3D'''.
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|Hello everyone. Welcome to this tutorial on '''Features of GChem3D'''.
  
 
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|00:07
 
|00:07
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|In this tutorial, we will learn about
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|In this tutorial, we will learn about:
  
 
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|00:10
 
|00:10
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|* Menu bar
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| Menu bar, File type formats
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|-
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|00:11
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|* File type formats
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|00:13
 
|00:13
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|* Various Model types and  
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| Various Model types and  
  
 
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|00:15
 
|00:15
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|how to  Change background color.
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|How to  Change background color.
  
 
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|00:18
 
|00:18
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|For this tutorial I am using '''Ubuntu Linux''' OS version  12.04.
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|For this tutorial, I am using '''Ubuntu Linux''' OS version  12.04,
  
 
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|00:24
 
|00:24
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|'''GChemPaint''' version 0.12.10.
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|'''GChemPaint''' version 0.12.10,
  
 
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|00:29
 
|00:29
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|'''GChem3D''' version 0.12.10
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|'''GChem3D''' version 0.12.10.
  
 
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|00:53
 
|00:53
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|To save the file click on '''Save''' icon on the tool bar.
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|To save the file, click on '''Save''' icon on the tool bar.
  
 
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|01:02
 
|01:02
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|To view the file in '''GChem3D''', it has to be saved in file formats like,
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|To view the file in '''GChem3D''', it has to be saved in file formats like '''.mol, .mdl''' and '''.pdb.'''
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'''.mol, .mdl''' and '''.pdb.'''
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|01:11
 
|01:11
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|Type the file name as '''Adenosine.pdb'''
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|Type the file name as '''Adenosine.pdb'''.
  
 
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|02:07
 
|02:07
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|Structures  drawn in '''GChemPaint''' can be viewed in '''GChem3D'''
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|Structures  drawn in '''GChemPaint''' can be viewed in '''GChem3D'''.
  
 
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|02:12
 
|02:12
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|To open '''GChem3D''' click on '''Dash Home'''.
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|To open '''GChem3D''', click on '''Dash Home'''.
  
 
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|02:40
 
|02:40
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|To open a file, Select ''' File''' click on '''Open'''.
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|To open a file, select ''' File'''. Click on '''Open'''.
  
 
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|03:17
 
|03:17
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|Default image size has '''Width''' ''300 pixels'' and '''Height''' ''300 pixels''.
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|Default image size has '''Width''' '300 pixels' and '''Height''' '300 pixels'.
  
 
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|03:29
 
|03:29
 
|Now to '''File type''' option.
 
|Now to '''File type''' option.
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|03:31
 
|03:31
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|04:48
 
|04:48
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|Right click on the file '''Adenosine.wrl'''.Choose option '''Open with Text Editor'''.
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|Right click on the file '''Adenosine.wrl'''. Choose option '''Open with Text Editor'''.
  
 
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|05:01
 
|05:01
 
|Now let us move on to ''' Page Setup'''.
 
|Now let us move on to ''' Page Setup'''.
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|05:04
 
|05:04
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|05:14
 
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|I had already discussed in the '''GChemPaint''' tutorials in this series
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|I had already discussed in the '''GChemPaint''' tutorials in this series.
  
 
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|05:32
 
|05:32
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|* Balls and sticks * Space filling
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| Balls and sticks * Space filling
  
 
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|05:35
 
|05:35
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|* Cylinders  and * Wireframe.  
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| Cylinders  and * Wireframe.  
  
 
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|05:58
 
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|'''Cylinders''' model shows the structure in the form of ''cylindrical pipes''.
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|'''Cylinders''' model shows the structure in the form of 'cylindrical pipes'.
  
 
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|06:03
 
|06:03
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|'''Wireframe''' model shows the ''skeletal'' structure.
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|'''Wireframe''' model shows the 'skeletal' structure.
  
 
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|06:21
 
|06:21
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|A submenu opens.
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|A sub-menu opens.
  
 
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|06:23
 
|06:23
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|Select '''Custom color''' at the end of submenu.
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|Select '''Custom color''' at the end of sub-menu.
  
 
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|Click on '''Ok''' button.Background color changes on the screen.
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|Click on '''OK''' button. Background color changes on the screen.
  
 
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|07:23
 
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|* Different Menus
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|Different Menus, File type formats
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|07:24
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|* File type formats
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|07:26
 
|07:26
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|* Model types and * How to Change background color.
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|Model types and * How to Change background color.
  
 
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|07:49
 
|07:49
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|Watch the video available at this URL.
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|Watch the video available at this URL.'''http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial'''
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'''http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial'''
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|More information on this Mission is available at this link.
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|More information on this Mission is available at this link.'''http://spoken-tutorial.org/NMEICT-Intro]'''
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'''http://spoken-tutorial.org/NMEICT-Intro]'''
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Latest revision as of 18:01, 27 March 2017

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, 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, 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

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