Difference between revisions of "Jmol-Application/C2/Modify-Display-and-View/English-timed"
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| − | |* Modify the view | + | |* Modify the '''view''' |
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| 00:19 | | 00:19 | ||
| − | |* Change the style of the display | + | |* Change the style of the '''display''' |
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| 00:22 | | 00:22 | ||
| − | |* Change the size and color of atoms and | + | |* Change the size and color of atoms and '''bond'''s |
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| 00:26 | | 00:26 | ||
| − | |* To display the model with axes and bound box. | + | |* To display the model with '''axes''' and '''bound box'''. |
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| 00:30 | | 00:30 | ||
| − | |* Save the image in various file | + | |* Save the image in various '''file format'''s. |
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| − | | '''Jmol Application''' | + | | '''Jmol Application''' window and |
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| 00:40 | | 00:40 | ||
| − | | know to create and edit | + | | know to '''create''' and '''edit model'''s using '''modelkit function'''. |
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| − | |* '''Ubuntu '''OS version | + | |* '''Ubuntu '''OS version 12.04 |
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| − | | To rotate the model, click on the “'''Rotate molecule'''” icon on the tool bar. | + | | To rotate the model, click on the “'''Rotate molecule'''” icon on the '''tool bar'''. |
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| − | |You can see the '''model''' is rotating. | + | |You can see that the '''model''' is rotating. |
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| − | |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'''. |
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| − | | For a detailed description, refer to the '''Mouse Manual''' provided in the Pop-up-menu. | + | | For a detailed description, refer to the '''Mouse Manual''' provided in the '''Pop-up-menu'''. |
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| 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'''. |
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| − | |Click on the | + | |Click on the panel to exit the Pop-up menu. |
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| 02:28 | | 02:28 | ||
| − | | To automatically | + | | To automatically '''spin''' the molecule on the panel, open the Pop-up menu. |
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| 02:44 | | 02:44 | ||
| − | | To turn off the spin, | + | | To turn off the spin, open the Pop-up-menu again. |
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| 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'''. |
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| 03:25 | | 03:25 | ||
| − | | '''View''' menu on the menu bar | + | | '''View''' menu on the menu bar has options to view the model from various angles. |
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| 04:44 | | 04:44 | ||
| − | | The style of display of molecular model can be modified in various ways. | + | | The style of display of '''molecular model''' can be modified in various ways. |
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| − | | Open the Pop-up-menu and select '''All''' | + | | Open the Pop-up-menu and select '''All'''. |
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| − | | We can display this model on screen with X, Y and Z axes and within a bounding box. | + | | We can display this model on the screen with X, Y and Z axes and within a bounding box. |
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| 07:31 | | 07:31 | ||
| − | | Open the Pop-up menu, select '''Style''' | + | | Open the Pop-up menu, select '''Style''' |
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| 07:34 | | 07:34 | ||
| − | | | + | |and Scroll down to '''Axes''' option. |
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| 07:44 | | 07:44 | ||
| − | | We now have the model on screen with all the axes. | + | | We now have the model on the screen with all the axes. |
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| 07:49 | | 07:49 | ||
| − | | To draw a bound box around the image, open the Pop-up-menu. | + | | To draw a '''bound box''' around the image, open the Pop-up-menu. |
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| 08:26 | | 08:26 | ||
| − | |* Rotate, zoom, move and spin the model on screen. | + | |* Rotate, zoom, move and spin the model on screen. |
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| 08:48 | | 08:48 | ||
| − | | | + | | For the Assignment- |
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| − | | Change the color of | + | | Change the color of hydrogens in the model to Green. |
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Revision as of 18:09, 3 June 2016
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| 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. |
