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{| border=1 | {| border=1 | ||
− | + | |'''Time''' | |
− | + | |'''Narration''' | |
|- | |- | ||
− | | 00:01 | + | |00:01 |
|Welcome to this tutorial on '''Modify Display and View '''in '''Jmol Application.''' | |Welcome to this tutorial on '''Modify Display and View '''in '''Jmol Application.''' | ||
|- | |- | ||
− | | 00:08 | + | |00:08 |
− | | In this tutorial, we will learn to: | + | |In this tutorial, we will learn to: |
|- | |- | ||
− | | 00:11 | + | |00:11 |
− | | | + | |Rotate, zoom, move and spin the model on screen |
|- | |- | ||
− | | 00:17 | + | |00:17 |
− | | | + | |Modify the '''view''' |
|- | |- | ||
− | | 00:19 | + | |00:19 |
− | | | + | |Change the style of the '''display''' |
|- | |- | ||
− | | 00:22 | + | |00:22 |
− | | | + | |Change the size and color of atoms and '''bond'''s |
|- | |- | ||
− | | 00:26 | + | |00:26 |
− | | | + | |To display the model with '''axes''' and '''bound box'''. |
|- | |- | ||
− | | 00:30 | + | |00:30 |
− | | | + | |Save the image in various '''file format'''s. |
|- | |- | ||
− | | 00:34 | + | |00:34 |
− | | To follow this tutorial, you should be familiar with | + | |To follow this tutorial, you should be familiar with |
|- | |- | ||
− | | 00:37 | + | |00:37 |
− | | | + | |'''Jmol Application''' window and |
|- | |- | ||
− | | 00:40 | + | |00:40 |
− | | know to create and edit | + | |know to '''create''' and '''edit model'''s using '''modelkit function'''. |
|- | |- | ||
− | | 00:45 | + | |00:45 |
|If not, watch the relevant tutorials available at the following link. | |If not, watch the relevant tutorials available at the following link. | ||
|- | |- | ||
− | | 00:51 | + | |00:51 |
− | | To record this tutorial, I am using: | + | |To record this tutorial, I am using: |
|- | |- | ||
− | | 00:53 | + | |00:53 |
− | | | + | |'''Ubuntu '''OS version 12.04 |
|- | |- | ||
− | | 00:58 | + | |00:58 |
− | | | + | |'''Jmol''' version 12.2.2 and |
|- | |- | ||
− | | 01:02 | + | |01:02 |
− | | | + | |'''Java''' version 7 |
|- | |- | ||
− | | 01:05 | + | |01:05 |
− | | I have opened a new '''Jmol '''window with a model of '''2-chloro-1-propanol '''on the '''panel'''. | + | |I have opened a new '''Jmol '''window with a model of '''2-chloro-1-propanol '''on the '''panel'''. |
|- | |- | ||
− | | 01:12 | + | |01:12 |
− | | We can rotate and zoom the model to get a better perspective of the structure. | + | |We can rotate and zoom the model to get a better perspective of the structure. |
|- | |- | ||
− | | 01:18 | + | |01:18 |
− | | | + | |To rotate the model, click on the “'''Rotate molecule'''” icon on the '''tool bar'''. |
|- | |- | ||
− | | 01:24 | + | |01:24 |
− | | | + | |Click on the model and observe that the cursor changes to a hand icon. |
|- | |- | ||
− | | 01:29 | + | |01:29 |
− | | Holding down the '''mouse button''', drag the '''mouse''' on the '''panel''' | + | |Holding down the '''mouse button''', drag the '''mouse''' on the '''panel''' |
|- | |- | ||
− | | 01:34 | + | |01:34 |
− | |You can see the '''model''' is rotating. | + | |You can see that the '''model''' is rotating. |
|- | |- | ||
− | | 01:37 | + | |01:37 |
− | | To zoom-in and zoom-out, place the cursor on the '''panel'''. | + | |To zoom-in and zoom-out, place the cursor on the '''panel'''. |
|- | |- | ||
− | | 01:42 | + | |01:42 |
− | |Move the '''mouse wheel''' upwards to zoom-out and downwards to zoom-in. | + | |Move the '''mouse wheel''' upwards to '''zoom-out''' and downwards to '''zoom-in'''. |
|- | |- | ||
− | | 01:49 | + | |01:49 |
− | | | + | |To move the model on the '''panel''', place the cursor on the model. |
|- | |- | ||
− | | 01:54 | + | |01:54 |
|Hold the '''Shift''' button on the keyboard. | |Hold the '''Shift''' button on the keyboard. | ||
|- | |- | ||
− | | 01:57 | + | |01:57 |
|Double-click and drag the '''mouse'''. | |Double-click and drag the '''mouse'''. | ||
|- | |- | ||
− | | 02:00 | + | |02:00 |
− | | | + | |For a detailed description, refer to the '''Mouse Manual''' provided in the '''Pop-up-menu'''. |
|- | |- | ||
− | | 02:06 | + | |02:06 |
− | |Open the Pop-up-menu and scroll down to '''About''' | + | |Open the Pop-up-menu and scroll down to '''About'''. Then select '''Jmol 12.2.2''' and click on '''Mouse Manual'''. |
|- | |- | ||
− | | 02:17 | + | |02:17 |
− | | If you are connected to the Internet, | + | |If you are connected to the Internet, |
|- | |- | ||
− | | 02:19 | + | |02:19 |
|a web page with “'''Mouse manual'''” appears on the screen. | |a web page with “'''Mouse manual'''” appears on the screen. | ||
|- | |- | ||
− | | 02:24 | + | |02:24 |
− | |Click on the | + | |Click on the panel to exit the Pop-up menu. |
|- | |- | ||
− | | 02:28 | + | |02:28 |
− | | To automatically | + | |To automatically '''spin''' the molecule on the panel, open the Pop-up menu. |
|- | |- | ||
− | | 02:34 | + | |02:34 |
|Scroll down to '''Spin''' and then click on option '''On'''. | |Scroll down to '''Spin''' and then click on option '''On'''. | ||
|- | |- | ||
− | | 02:40 | + | |02:40 |
− | | We can see that the model is spinning on the '''panel'''. | + | |We can see that the model is spinning on the '''panel'''. |
|- | |- | ||
− | | 02:44 | + | |02:44 |
− | | | + | |To turn off the spin, open the Pop-up-menu again. |
|- | |- | ||
− | | 02:49 | + | |02:49 |
|Scroll down to '''Spin''' and click on '''Off'''. | |Scroll down to '''Spin''' and click on '''Off'''. | ||
|- | |- | ||
− | | 02:54 | + | |02:54 |
− | | | + | |As an assignment- |
|- | |- | ||
− | | 02:56 | + | |02:56 |
− | | Create a model of '''2-chloro-3-Iodo-pentane'''. | + | |Create a model of '''2-chloro-3-Iodo-pentane'''. |
|- | |- | ||
− | | 03:00 | + | |03:00 |
− | | Explore the '''Spin''' option in the Pop-up menu. | + | |Explore the '''Spin''' option in the Pop-up menu. |
|- | |- | ||
− | | 03:04 | + | |03:04 |
− | | Change the direction of spin to '''Z''' | + | |Change the direction of spin to '''Z-axis''' and rate of spin to '''40'''. |
|- | |- | ||
− | | 03:10 | + | |03:10 |
− | | As a hint: Use '''Set Z Rate '''option in the pop-up menu | + | |As a hint: Use '''Set Z Rate '''option in the pop-up menu. |
|- | |- | ||
− | | 03:16 | + | |03:16 |
|Your completed assignment should look as follows. | |Your completed assignment should look as follows. | ||
|- | |- | ||
− | | 03:22 | + | |03:22 |
− | | | + | |Let us now learn about the '''View''' menu. |
|- | |- | ||
− | | 03:25 | + | |03:25 |
− | | | + | |'''View''' menu on the menu bar has options to view the model from various angles. |
|- | |- | ||
− | | 03:31 | + | |03:31 |
− | | | + | |Click on the '''View''' menu. |
|- | |- | ||
− | | 03:33 | + | |03:33 |
− | | | + | |Scroll down the menu and choose from the various options provided. |
|- | |- | ||
− | | 03:38 | + | |03:38 |
− | | | + | |For example, I will choose '''Top''' view. |
|- | |- | ||
− | | 03:42 | + | |03:42 |
|Click on the '''Top''' option. | |Click on the '''Top''' option. | ||
|- | |- | ||
− | | 03:45 | + | |03:45 |
− | | | + | |The '''image''' on the '''screen''' shows how the molecule looks from the top. |
|- | |- | ||
− | | 03:50 | + | |03:50 |
− | | | + | |We can '''save''' this '''view''' as an image in various file formats. |
|- | |- | ||
− | | 03:55 | + | |03:55 |
− | | | + | |Click on the '''Save current view as an image''' icon. |
|- | |- | ||
− | | 03:59 | + | |03:59 |
− | | | + | |A '''Save''' dialog box appears. |
|- | |- | ||
− | | 04:03 | + | |04:03 |
− | | | + | |To select the file format, scroll down the options on the '''Image Type'''. |
|- | |- | ||
− | | 04:09 | + | |04:09 |
− | | | + | |I will select '''JPEG''' format. |
|- | |- | ||
− | | 04:13 | + | |04:13 |
|Open the folder in which you want the file to be saved. | |Open the folder in which you want the file to be saved. | ||
|- | |- | ||
− | | 04:17 | + | |04:17 |
− | | | + | |I want it on '''Desktop.''' |
|- | |- | ||
− | | 04:19 | + | |04:19 |
|Select '''Desktop''' and click on '''Open''' button. | |Select '''Desktop''' and click on '''Open''' button. | ||
|- | |- | ||
− | | 04:24 | + | |04:24 |
− | | | + | |In the '''File Name '''text-box, type '''“2-chloro-1-propanol” '''. |
|- | |- | ||
− | | 04:30 | + | |04:30 |
− | | | + | |Go to “'''Files of Type'''” and select '''jpg'''. |
|- | |- | ||
− | | 04:35 | + | |04:35 |
− | | | + | |Click on '''Save '''button. |
|- | |- | ||
− | | 04:38 | + | |04:38 |
− | | | + | |The image will now be saved in '''JPEG '''format on the '''Desktop'''. |
|- | |- | ||
− | | 04:44 | + | |04:44 |
− | | | + | |The style of display of '''molecular model''' can be modified in various ways. |
|- | |- | ||
− | | 04:50 | + | |04:50 |
|Size and color of atoms and '''bond'''s in this molecule can be changed, if required. | |Size and color of atoms and '''bond'''s in this molecule can be changed, if required. | ||
|- | |- | ||
− | | 04:57 | + | |04:57 |
− | | | + | |We have an option to modify all the atoms in the molecule or a select set. |
|- | |- | ||
− | | 05:03 | + | |05:03 |
− | | | + | |The default display of the model on the panel is of '''ball and stick.''' |
|- | |- | ||
− | | 05:09 | + | |05:09 |
− | | | + | |To change the display into '''CPK Space fill''', open the Pop-up-menu. |
|- | |- | ||
− | | 05:15 | + | |05:15 |
− | | | + | |Go to '''Select''' and click on '''All''' to modify the whole molecule. |
|- | |- | ||
− | | 05:22 | + | |05:22 |
− | | | + | |Open the Pop-up-menu again. |
|- | |- | ||
− | | 05:25 | + | |05:25 |
|Scroll down to '''Style''', select '''Scheme''' from the sub-menu. | |Scroll down to '''Style''', select '''Scheme''' from the sub-menu. | ||
|- | |- | ||
− | | 05:30 | + | |05:30 |
− | | | + | |And click on '''CPK Spacefill''' option. |
|- | |- | ||
− | | 05:35 | + | |05:35 |
− | | | + | |The model on the screen is converted to '''CPK Spacefill''' model. |
|- | |- | ||
− | | 05:40 | + | |05:40 |
|Let us now convert it back to '''ball and stick''' model. | |Let us now convert it back to '''ball and stick''' model. | ||
|- | |- | ||
− | | 05:44 | + | |05:44 |
− | | | + | |Let's follow the same steps as before. |
|- | |- | ||
|05:48 | |05:48 | ||
− | | Open the Pop-up-menu. | + | |Open the Pop-up-menu. |
|- | |- | ||
− | | 05:50 | + | |05:50 |
|Scroll down to '''Style''', select '''Scheme''' and click on '''Ball and Stick''' option. | |Scroll down to '''Style''', select '''Scheme''' and click on '''Ball and Stick''' option. | ||
|- | |- | ||
− | | 05:56 | + | |05:56 |
− | | | + | |The model is now converted to''' ball and stick '''style display. |
|- | |- | ||
− | | 06:01 | + | |06:01 |
− | | | + | |The size of the bonds can be changed using Pop-up menu, as well as '''Display''' menu on the menu bar. |
|- | |- | ||
− | | 06:08 | + | |06:08 |
|Click on the '''Display''' menu and select '''Bond'''. | |Click on the '''Display''' menu and select '''Bond'''. | ||
|- | |- | ||
− | | 06:12 | + | |06:12 |
|The sub-menu has options of bonds in different size diameter, in '''angstrom units. ''' | |The sub-menu has options of bonds in different size diameter, in '''angstrom units. ''' | ||
|- | |- | ||
− | | 06:19 | + | |06:19 |
− | | | + | |For example, I will select '''0.1 Angstrom''' and click on it. |
|- | |- | ||
− | | 06:26 | + | |06:26 |
− | | | + | |Note the change in the thickness of the bonds. |
|- | |- | ||
− | | 06:30 | + | |06:30 |
− | | | + | |We can also change the colour of atoms and bonds. |
|- | |- | ||
− | | 06:34 | + | |06:34 |
− | | | + | |I want to change the colour of all the '''Carbon''' atoms in the model to yellow. |
|- | |- | ||
− | | 06:39 | + | |06:39 |
− | | | + | |To do this, open the Pop-up menu and go to '''Select'''. |
|- | |- | ||
− | | 06:44 | + | |06:44 |
− | | | + | |Scroll down to '''Element''' and click on '''Carbon'''. |
|- | |- | ||
− | | 06:48 | + | |06:48 |
− | | | + | |Open the Pop-up menu again and select '''Color'''. |
|- | |- | ||
− | | 06:52 | + | |06:52 |
|Then select '''Atoms''' and click on '''Yellow''' option. | |Then select '''Atoms''' and click on '''Yellow''' option. | ||
|- | |- | ||
|06:57 | |06:57 | ||
− | + | |All the '''Carbons''' in the model, now appear yellow in colour. | |
|- | |- | ||
− | | 07:02 | + | |07:02 |
− | | | + | |Let's see how to change the color of bonds. |
|- | |- | ||
− | | 07:06 | + | |07:06 |
− | | | + | |Open the Pop-up-menu and select '''All'''. |
|- | |- | ||
− | | 07:10 | + | |07:10 |
− | | | + | |Open the Pop-up-menu again. |
|- | |- | ||
− | | 07:12 | + | |07:12 |
|Scroll down to '''Color''', select '''Bonds''' from the sub-menu. | |Scroll down to '''Color''', select '''Bonds''' from the sub-menu. | ||
|- | |- | ||
− | | 07:16 | + | |07:16 |
− | | | + | |Scroll down and click on '''Blue''' option. |
|- | |- | ||
− | | 07:20 | + | |07:20 |
− | | | + | |All the bonds are now blue in color. |
|- | |- | ||
− | | 07:23 | + | |07:23 |
− | | | + | |We can display this model on the screen with X, Y and Z axes and within a bounding box. |
|- | |- | ||
− | | 07:31 | + | |07:31 |
− | | | + | |Open the Pop-up menu, select '''Style''' |
|- | |- | ||
− | | 07:34 | + | |07:34 |
− | | | + | |and Scroll down to '''Axes''' option. |
|- | |- | ||
− | | 07:37 | + | |07:37 |
− | | | + | |From the sub-menu select '''Pixel Width '''. |
|- | |- | ||
− | | 07:40 | + | |07:40 |
− | | | + | |I will choose '''3 px.''' as pixel width. |
|- | |- | ||
− | | 07:44 | + | |07:44 |
− | | | + | |We now have the model on the screen with all the axes. |
|- | |- | ||
− | | 07:49 | + | |07:49 |
− | | | + | |To draw a '''bound box''' around the image, open the Pop-up-menu. |
|- | |- | ||
− | | 07:54 | + | |07:54 |
|Scroll down to '''Style''' and select '''Boundbox''' from the options. | |Scroll down to '''Style''' and select '''Boundbox''' from the options. | ||
|- | |- | ||
− | | 07:59 | + | |07:59 |
|Select '''Pixel width''' and click on the pixel width '''3 px'''. | |Select '''Pixel width''' and click on the pixel width '''3 px'''. | ||
|- | |- | ||
− | | 08:05 | + | |08:05 |
− | | | + | |On the screen, we have the model of '''2-chloro-1-propanol''' in '''Boundbox''' with '''Axes.''' |
|- | |- | ||
− | | 08:12 | + | |08:12 |
|To view the '''Boundbox''' clearly, we may have to zoom-in or zoom out. | |To view the '''Boundbox''' clearly, we may have to zoom-in or zoom out. | ||
|- | |- | ||
− | | 08:17 | + | |08:17 |
− | | | + | |'''Save''' the '''image''' and exit the program. |
|- | |- | ||
− | | 08:21 | + | |08:21 |
− | | | + | |Let's summarize what we have learnt. |
|- | |- | ||
− | | 08:23 | + | |08:23 |
|In this tutorial, we have learnt to: | |In this tutorial, we have learnt to: | ||
|- | |- | ||
− | | 08:26 | + | |08:26 |
− | | | + | |Rotate, zoom, move and spin the model on screen. |
|- | |- | ||
− | | 08:31 | + | |08:31 |
− | | | + | |View the model from various angles. |
|- | |- | ||
− | | 08:34 | + | |08:34 |
− | | | + | |Change the style of the display. |
|- | |- | ||
− | | 08:36 | + | |08:36 |
− | | | + | |Change the color of atoms and bonds. |
|- | |- | ||
|08:39 | |08:39 | ||
− | | We have also learnt to: | + | |We have also learnt to: |
|- | |- | ||
− | | 08:41 | + | |08:41 |
− | | | + | |Display the image with axes and boundbox and |
|- | |- | ||
− | | 08:44 | + | |08:44 |
− | | | + | |Save the image in different file formats. |
|- | |- | ||
− | | 08:48 | + | |08:48 |
− | | | + | |For the Assignment- |
|- | |- | ||
− | | 08:50 | + | |08:50 |
|Create a model of '''3-amino-1-propanol.''' | |Create a model of '''3-amino-1-propanol.''' | ||
|- | |- | ||
− | | 08:53 | + | |08:53 |
− | | Change the display to '''Sticks'''. | + | |Change the display to '''Sticks'''. |
|- | |- | ||
− | | 08:56 | + | |08:56 |
− | | Change the color of | + | |Change the color of hydrogens in the model to Green. |
|- | |- | ||
− | | 09:00 | + | |09:00 |
− | | Change the color of all the bonds to yellow. | + | |Change the color of all the bonds to yellow. |
|- | |- | ||
− | | 09:04 | + | |09:04 |
|Your completed assignment should look as follows. | |Your completed assignment should look as follows. | ||
|- | |- | ||
− | | 09:12 | + | |09:12 |
− | | Watch the video available at the following link. | + | |Watch the video available at the following link. |
|- | |- | ||
− | | 09:15 | + | |09:15 |
|It summarizes the Spoken Tutorial project. | |It summarizes the Spoken Tutorial project. | ||
|- | |- | ||
− | | 09:19 | + | |09:19 |
|If you do not have good bandwidth, you can download and watch it. | |If you do not have good bandwidth, you can download and watch it. | ||
|- | |- | ||
− | | 09:24 | + | |09:24 |
− | | | + | |The Spoken Tutorial Project team: |
|- | |- | ||
− | | 09:26 | + | |09:26 |
− | | | + | |Conducts workshops using spoken tutorials. |
|- | |- | ||
− | | 09:29 | + | |09:29 |
− | | | + | |Gives certificates to those who pass an on-line test. |
|- | |- | ||
− | | 09:34 | + | |09:34 |
− | |For more details, please write to: contact@spoken-tutorial.org | + | |For more details, please write to: '''contact@spoken-tutorial.org''' |
|- | |- | ||
− | | 09:41 | + | |09:41 |
|'''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project. | |'''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project. | ||
|- | |- | ||
− | | 09:44 | + | |09:44 |
|It is supported by the National Mission on Education through ICT, MHRD, Government of India. | |It is supported by the National Mission on Education through ICT, MHRD, Government of India. | ||
|- | |- | ||
− | | 09:51 | + | |09:51 |
|More information on this mission is available at the following link. | |More information on this mission is available at the following link. | ||
|- | |- | ||
− | | 09:57 | + | |09:57 |
− | | This is Snehalatha from IIT Bombay, signing off. Thank you for joining. | + | |This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining. |
− | + | ||
|} | |} |
Latest revision as of 16:31, 28 March 2017
Time | Narration |
00:01 | Welcome to this tutorial on Modify Display and View in Jmol Application. |
00:08 | In this tutorial, we will learn to: |
00:11 | Rotate, zoom, move and spin the model on screen |
00:17 | Modify the view |
00:19 | Change the style of the display |
00:22 | Change the size and color of atoms and bonds |
00:26 | To display the model with axes and bound box. |
00:30 | Save the image in various file formats. |
00:34 | To follow this tutorial, you should be familiar with |
00:37 | Jmol Application window and |
00:40 | know to create and edit models using modelkit function. |
00:45 | If not, watch the relevant tutorials available at the following link. |
00:51 | To record this tutorial, I am using: |
00:53 | Ubuntu OS version 12.04 |
00:58 | Jmol version 12.2.2 and |
01:02 | Java version 7 |
01:05 | I have opened a new Jmol window with a model of 2-chloro-1-propanol on the panel. |
01:12 | We can rotate and zoom the model to get a better perspective of the structure. |
01:18 | To rotate the model, click on the “Rotate molecule” icon on the tool bar. |
01:24 | Click on the model and observe that the cursor changes to a hand icon. |
01:29 | Holding down the mouse button, drag the mouse on the panel |
01:34 | You can see that the model is rotating. |
01:37 | To zoom-in and zoom-out, place the cursor on the panel. |
01:42 | Move the mouse wheel upwards to zoom-out and downwards to zoom-in. |
01:49 | To move the model on the panel, place the cursor on the model. |
01:54 | Hold the Shift button on the keyboard. |
01:57 | Double-click and drag the mouse. |
02:00 | For a detailed description, refer to the Mouse Manual provided in the Pop-up-menu. |
02:06 | Open the Pop-up-menu and scroll down to About. Then select Jmol 12.2.2 and click on Mouse Manual. |
02:17 | If you are connected to the Internet, |
02:19 | a web page with “Mouse manual” appears on the screen. |
02:24 | Click on the panel to exit the Pop-up menu. |
02:28 | To automatically spin the molecule on the panel, open the Pop-up menu. |
02:34 | Scroll down to Spin and then click on option On. |
02:40 | We can see that the model is spinning on the panel. |
02:44 | To turn off the spin, open the Pop-up-menu again. |
02:49 | Scroll down to Spin and click on Off. |
02:54 | As an assignment- |
02:56 | Create a model of 2-chloro-3-Iodo-pentane. |
03:00 | Explore the Spin option in the Pop-up menu. |
03:04 | Change the direction of spin to Z-axis and rate of spin to 40. |
03:10 | As a hint: Use Set Z Rate option in the pop-up menu. |
03:16 | Your completed assignment should look as follows. |
03:22 | Let us now learn about the View menu. |
03:25 | View menu on the menu bar has options to view the model from various angles. |
03:31 | Click on the View menu. |
03:33 | Scroll down the menu and choose from the various options provided. |
03:38 | For example, I will choose Top view. |
03:42 | Click on the Top option. |
03:45 | The image on the screen shows how the molecule looks from the top. |
03:50 | We can save this view as an image in various file formats. |
03:55 | Click on the Save current view as an image icon. |
03:59 | A Save dialog box appears. |
04:03 | To select the file format, scroll down the options on the Image Type. |
04:09 | I will select JPEG format. |
04:13 | Open the folder in which you want the file to be saved. |
04:17 | I want it on Desktop. |
04:19 | Select Desktop and click on Open button. |
04:24 | In the File Name text-box, type “2-chloro-1-propanol” . |
04:30 | Go to “Files of Type” and select jpg. |
04:35 | Click on Save button. |
04:38 | The image will now be saved in JPEG format on the Desktop. |
04:44 | The style of display of molecular model can be modified in various ways. |
04:50 | Size and color of atoms and bonds in this molecule can be changed, if required. |
04:57 | We have an option to modify all the atoms in the molecule or a select set. |
05:03 | The default display of the model on the panel is of ball and stick. |
05:09 | To change the display into CPK Space fill, open the Pop-up-menu. |
05:15 | Go to Select and click on All to modify the whole molecule. |
05:22 | Open the Pop-up-menu again. |
05:25 | Scroll down to Style, select Scheme from the sub-menu. |
05:30 | And click on CPK Spacefill option. |
05:35 | The model on the screen is converted to CPK Spacefill model. |
05:40 | Let us now convert it back to ball and stick model. |
05:44 | Let's follow the same steps as before. |
05:48 | Open the Pop-up-menu. |
05:50 | Scroll down to Style, select Scheme and click on Ball and Stick option. |
05:56 | The model is now converted to ball and stick style display. |
06:01 | The size of the bonds can be changed using Pop-up menu, as well as Display menu on the menu bar. |
06:08 | Click on the Display menu and select Bond. |
06:12 | The sub-menu has options of bonds in different size diameter, in angstrom units. |
06:19 | For example, I will select 0.1 Angstrom and click on it. |
06:26 | Note the change in the thickness of the bonds. |
06:30 | We can also change the colour of atoms and bonds. |
06:34 | I want to change the colour of all the Carbon atoms in the model to yellow. |
06:39 | To do this, open the Pop-up menu and go to Select. |
06:44 | Scroll down to Element and click on Carbon. |
06:48 | Open the Pop-up menu again and select Color. |
06:52 | Then select Atoms and click on Yellow option. |
06:57 | All the Carbons in the model, now appear yellow in colour. |
07:02 | Let's see how to change the color of bonds. |
07:06 | Open the Pop-up-menu and select All. |
07:10 | Open the Pop-up-menu again. |
07:12 | Scroll down to Color, select Bonds from the sub-menu. |
07:16 | Scroll down and click on Blue option. |
07:20 | All the bonds are now blue in color. |
07:23 | We can display this model on the screen with X, Y and Z axes and within a bounding box. |
07:31 | Open the Pop-up menu, select Style |
07:34 | and Scroll down to Axes option. |
07:37 | From the sub-menu select Pixel Width . |
07:40 | I will choose 3 px. as pixel width. |
07:44 | We now have the model on the screen with all the axes. |
07:49 | To draw a bound box around the image, open the Pop-up-menu. |
07:54 | Scroll down to Style and select Boundbox from the options. |
07:59 | Select Pixel width and click on the pixel width 3 px. |
08:05 | On the screen, we have the model of 2-chloro-1-propanol in Boundbox with Axes. |
08:12 | To view the Boundbox clearly, we may have to zoom-in or zoom out. |
08:17 | Save the image and exit the program. |
08:21 | Let's summarize what we have learnt. |
08:23 | In this tutorial, we have learnt to: |
08:26 | Rotate, zoom, move and spin the model on screen. |
08:31 | View the model from various angles. |
08:34 | Change the style of the display. |
08:36 | Change the color of atoms and bonds. |
08:39 | We have also learnt to: |
08:41 | Display the image with axes and boundbox and |
08:44 | Save the image in different file formats. |
08:48 | For the Assignment- |
08:50 | Create a model of 3-amino-1-propanol. |
08:53 | Change the display to Sticks. |
08:56 | Change the color of hydrogens in the model to Green. |
09:00 | Change the color of all the bonds to yellow. |
09:04 | Your completed assignment should look as follows. |
09:12 | Watch the video available at the following link. |
09:15 | It summarizes the Spoken Tutorial project. |
09:19 | If you do not have good bandwidth, you can download and watch it. |
09:24 | The Spoken Tutorial Project team: |
09:26 | Conducts workshops using spoken tutorials. |
09:29 | Gives certificates to those who pass an on-line test. |
09:34 | For more details, please write to: contact@spoken-tutorial.org |
09:41 | Spoken Tutorial project is a part of the Talk to a Teacher project. |
09:44 | It is supported by the National Mission on Education through ICT, MHRD, Government of India. |
09:51 | More information on this mission is available at the following link. |
09:57 | This is Snehalatha from IIT Bombay, signing off. Thank you for joining. |