Difference between revisions of "Jmol-Application/C2/Structures-from-Database/English-timed"
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| − | | The ''''File'''' menu on the menu bar has an option | + | | The ''''File'''' menu on the menu bar has an option '''Get MOL.''' |
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| 01:12 | | 01:12 | ||
| − | | This loads molecules from chemical structure database | + | | This loads molecules from chemical structure database '''PubChem.''' |
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| 01:17 | | 01:17 | ||
| − | | It also has another option | + | | It also has another option '''Get PDB''' to load '''protein''' structures from '''Protein Data Bank'''. |
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| 01:26 | | 01:26 | ||
| − | | This feature will be explained in detail in another tutorial. | + | | This feature will be explained in detail, in another tutorial. |
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| 01:31 | | 01:31 | ||
| − | | To load a chemical structure on the panel, click on | + | | To '''load''' a chemical structure on the panel, click on '''Get Mol'''. |
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| 01:36 | | 01:36 | ||
| − | | An | + | | An '''Input''' dialog-box opens on the '''screen'''. |
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| 06:51 | | 06:51 | ||
| − | | A '''3D model''' of | + | | A '''3D model''' of '''Alanine''' opens on screen. |
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| 06:55 | | 06:55 | ||
| − | | Open the '''modelkit''' menu and click on | + | | Open the '''modelkit''' menu and click on '''fix hydrogens and minimize''' option. |
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| 07:08 | | 07:08 | ||
| − | | As with any | + | | As with any ".mol" file, we can change the display using menu bar and also '''Pop-up '''menu. |
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| 08:57 | | 08:57 | ||
| − | | This is Snehalatha from IIT Bombay, signing off. Thank you for joining. | + | | This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining. |
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Revision as of 17:42, 28 May 2016
| Time | Narration |
| 00:01 | Welcome to this tutorial on Structures from Database in Jmol. |
| 00:07 | In this tutorial, we will learn to: |
| 00:10 | * Load chemical structures from PubChem database and |
| 00:14 | * Convert 2D structures drawn in GChemPaint to 3D models in Jmol. |
| 00:21 | To follow this tutorial, you should be familiar with Jmol Application. |
| 00:27 | If not, watch the relevant tutorials available at our website. |
| 00:33 | To record this tutorial, I am using: |
| 00:35 | * Ubuntu Linux OS version. 12.04 |
| 00:40 | * Jmol version 12.2.2 |
| 00:44 | * Java version 7. |
| 00:46 | * GChemPaint version 0.12.10 |
| 00:51 | * Mozilla Firefox browser 22.0 |
| 00:56 | I have opened a new Jmol Application window. |
| 01:00 | Jmol has a feature to load structures of compounds listed in the database. |
| 01:07 | The 'File' menu on the menu bar has an option Get MOL. |
| 01:12 | This loads molecules from chemical structure database PubChem. |
| 01:17 | It also has another option Get PDB to load protein structures from Protein Data Bank. |
| 01:26 | This feature will be explained in detail, in another tutorial. |
| 01:31 | To load a chemical structure on the panel, click on Get Mol. |
| 01:36 | An Input dialog-box opens on the screen. |
| 01:40 | Any molecule listed in the database can be loaded by typing the following in the text box: |
| 01:48 | Common name or IUPAC name, |
| 01:51 | CAS number, |
| 01:54 | CID number, |
| 01:56 | InChi identifier or |
| 01:58 | SMILES identifier. |
| 02:01 | Please visit Pubchem database website for information on identification numbers for a particular chemical. |
| 02:09 | Let us display phenol on screen. |
| 02:13 | So, type: "phenol" in the Input text-box. |
| 02:16 | click on OK button. |
| 02:20 | A Model of phenol is displayed on the panel. |
| 02:24 | We can modify the display of phenol using various rendering options. |
| 02:30 | These options are listed in the Menu bar and Pop-up menu. |
| 02:36 | We can add substituents to the benzene ring of phenol. |
| 02:41 | First, let us label the atoms in the model. |
| 02:45 | Click on the Display menu and select Label. Click on Number option. |
| 02:52 | Now, let's replace a hydrogen number 10 attached to the carbon atom number 4 with an amino group. |
| 03:00 | Open the modelkit menu, select nitrogen from the options. |
| 03:06 | Click on hydrogen number 10. |
| 03:09 | This is a molecule of Para-Amino Phenol on the panel. |
| 03:14 | We will change the display to Sticks display. |
| 03:18 | Exit the modelkit menu. |
| 03:21 | Open the Pop-up menu, scroll down to Style , select Scheme and click on Sticks options. |
| 03:30 | On the panel, we have a model of Para-Amino-phenol in sticks display. |
| 03:36 | Complex structures which are difficult to create, can easily be loaded on the panel. |
| 03:42 | For example: cholesterol. |
| 03:45 | Click on File menu. |
| 03:47 | Click on Get Mol option. In the text-box, type: Cholesterol . |
| 03:54 | click on OK button. |
| 03:57 | A molecule of Cholesterol is displayed on the panel. |
| 04:02 | We can highlight the features like double-bond and side-chain in the molecule. |
| 04:08 | To highlight double-bond, let us first change the color of carbon atoms of the double-bond. |
| 04:15 | Click on Select atoms icon in the tool bar. |
| 04:19 | Then click on the carbon atoms involved in the double-bond. |
| 04:24 | A yellow halo appears around the atoms. |
| 04:28 | Open the Pop-up-menu. |
| 04:30 | Scroll down to Color, select Atoms and click on Orange option. |
| 04:37 | Now click on “Rotate molecule” option in the tool bar. |
| 04:42 | The double-bond in the cholesterol model is now in orange color. |
| 04:49 | Similarly, we can highlight the carbons in the side-chain. |
| 04:54 | Using Pop-up-menu change the color to violet. |
| 04:59 | On the panel, we have a model of Cholesterol with important features highlighted. |
| 05:06 | As an assignment- |
| 05:08 | * Load structure of caffeine from Pubchem database. |
| 05:11 | * Highlight the important features in the molecule. |
| 05:15 | * Modify the display to wireframe. |
| 05:19 | Now I will discuss another important feature of Jmol. |
| 05:24 | We can convert 2D structures of molecules, drawn in another software, into 3D models. |
| 05:31 | Here, I have a model of aminoacid Alanine on the panel. |
| 05:36 | 2D structure of this molecule was drawn in software called GChemPaint. |
| 05:42 | The structure was saved as a ".mol" file. |
| 05:46 | GchemPaint is an Open source software for drawing 2D chemical structures. |
| 05:51 | Tutorials on GChemPaint are available at the following link. |
| 05:56 | To draw structures and save in ".mol" format, refer to Analysis of Compounds tutorial. |
| 06:05 | Shown on this Gchempaint display area are 2D drawings of- |
| 06:10 | * Amino acid -Alanine |
| 06:12 | * Nuclioside -Adenosine |
| 06:14 | * Saccharide -Alpha-D glucopyranose. |
| 06:19 | I have saved them in '.mol' format on my Desktop. |
| 06:24 | First let's view the 2D structure of Alanine as 3D model, in Jmol Application. |
| 06:32 | So, I will open a new Jmol window. |
| 06:36 | Click on Open a file icon in the tool bar. |
| 06:40 | I will choose Desktop folder and click on Open. Choose the file 'Alanine.mol' and click on Open button. |
| 06:51 | A 3D model of Alanine opens on screen. |
| 06:55 | Open the modelkit menu and click on fix hydrogens and minimize option. |
| 07:03 | Hydrogens are added to the structure and the energy minimized. |
| 07:08 | As with any ".mol" file, we can change the display using menu bar and also Pop-up menu. |
| 07:15 | Here is the 3D model of Adenosine.mol in Jmol. |
| 07:19 | And this is a 3D model of Alpha-D-glucopyranose.mol in Jmol. |
| 07:25 | Let's summarize. |
| 07:27 | In this tutorial, we have learnt to: |
| 07:32 | * Load chemical structures from Pubchem data base. |
| 07:34 | * Modify the display of Phenol and Cholesterol. |
| 07:38 | * Convert 2D structures drawn in GChemPaint to 3D models in Jmol. |
| 07:44 | * Convert 2D structures of Alanine, Adenosine and Alpha-D-glucopyranose to 3D models. |
| 07:53 | Here is another assignment for you. |
| 07:56 | # Draw 2D structures of the following Amino acids in GChemPaint- |
| 08:01 | * Cysteine |
| 08:03 | * Histidine |
| 08:04 | * Phenylalanine |
| 08:06 | # Save as '.mol' files. |
| 08:09 | # Open the files in Jmol and modify the display. |
| 08:12 | Watch the video available at this URL. |
| 08:16 | It summarizes the Spoken Tutorial project. |
| 08:19 | If you do not have good bandwidth, you can download and watch it. |
| 08:23 | The Spoken Tutorial Project team: |
| 08:26 | * Conducts workshops using spoken tutorials. |
| 08:29 | * Gives certificates to those who pass an on-line test. |
| 08:33 | For more details, please write to:
contact@spoken-tutorial.org |
| 08:40 | Spoken Tutorial project is a part of the Talk to a Teacher project. |
| 08:45 | It is supported by the National Mission on Education through ICT, MHRD, Government of India. |
| 08:52 | More information on this mission is available at this link: |
| 08:57 | This is Snehalatha from IIT Bombay, signing off. Thank you for joining. |
