Difference between revisions of "GChemPaint/C3/Features-of-GChem3D/English-timed"
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{|border=1 | {|border=1 | ||
|'''Time''' | |'''Time''' | ||
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|00:01 | |00:01 | ||
− | |Hello everyone.Welcome to this tutorial on '''Features of GChem3D'''. | + | |Hello everyone. Welcome to this tutorial on '''Features of GChem3D'''. |
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|00:07 | |00:07 | ||
− | |In this tutorial, we will learn about | + | |In this tutorial, we will learn about: |
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|00:10 | |00:10 | ||
− | | | + | | Menu bar, File type formats |
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− | + | ||
− | + | ||
− | + | ||
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|00:13 | |00:13 | ||
− | | | + | | Various Model types and |
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|00:15 | |00:15 | ||
− | | | + | |How to Change background color. |
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|00:18 | |00:18 | ||
− | |For this tutorial | + | |For this tutorial, I am using '''Ubuntu Linux''' OS version 12.04, |
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|00:24 | |00:24 | ||
− | |'''GChemPaint''' version 0.12.10 | + | |'''GChemPaint''' version 0.12.10, |
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|00:29 | |00:29 | ||
− | |'''GChem3D''' version 0.12.10 | + | |'''GChem3D''' version 0.12.10. |
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|00:53 | |00:53 | ||
− | |To save the file click on '''Save''' icon on the tool bar. | + | |To save the file, click on '''Save''' icon on the tool bar. |
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|01:02 | |01:02 | ||
− | |To view the file in '''GChem3D''', it has to be saved in file formats like | + | |To view the file in '''GChem3D''', it has to be saved in file formats like '''.mol, .mdl''' and '''.pdb.''' |
− | '''.mol, .mdl''' and '''.pdb.''' | + | |
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|01:11 | |01:11 | ||
− | |Type the file name as '''Adenosine.pdb''' | + | |Type the file name as '''Adenosine.pdb'''. |
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|02:07 | |02:07 | ||
− | |Structures drawn in '''GChemPaint''' can be viewed in '''GChem3D''' | + | |Structures drawn in '''GChemPaint''' can be viewed in '''GChem3D'''. |
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|02:12 | |02:12 | ||
− | |To open '''GChem3D''' click on '''Dash Home'''. | + | |To open '''GChem3D''', click on '''Dash Home'''. |
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|02:40 | |02:40 | ||
− | |To open a file, | + | |To open a file, select ''' File'''. Click on '''Open'''. |
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|03:17 | |03:17 | ||
− | |Default image size has '''Width | + | |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 | ||
− | |Right click on the file '''Adenosine.wrl'''.Choose option '''Open with Text Editor'''. | + | |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 | |05:14 | ||
− | |I had already discussed in the '''GChemPaint''' tutorials in this series | + | |I had already discussed in the '''GChemPaint''' tutorials in this series. |
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|05:32 | |05:32 | ||
− | | | + | | Balls and sticks * Space filling |
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|05:35 | |05:35 | ||
− | | | + | | Cylinders and * Wireframe. |
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|05:58 | |05:58 | ||
− | |'''Cylinders''' model shows the structure in the form of | + | |'''Cylinders''' model shows the structure in the form of 'cylindrical pipes'. |
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|06:03 | |06:03 | ||
− | |'''Wireframe''' model shows the | + | |'''Wireframe''' model shows the 'skeletal' structure. |
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|06:21 | |06:21 | ||
− | |A | + | |A sub-menu opens. |
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|06:23 | |06:23 | ||
− | |Select '''Custom color''' at the end of | + | |Select '''Custom color''' at the end of sub-menu. |
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|07:11 | |07:11 | ||
− | |Click on ''' | + | |Click on '''OK''' button. Background color changes on the screen. |
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|07:23 | |07:23 | ||
− | | | + | |Different Menus, File type formats |
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|07:26 | |07:26 | ||
− | | | + | |Model types and * How to Change background color. |
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|07:49 | |07:49 | ||
− | |Watch the video available at this URL. | + | |Watch the video available at this URL.'''http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial''' |
− | '''http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial''' | + | |
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|08:29 | |08:29 | ||
− | |More information on this Mission is available at this link. | + | |More information on this Mission is available at this link.'''http://spoken-tutorial.org/NMEICT-Intro]''' |
− | '''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. |