Difference between revisions of "Jmol-Application/C2/Structures-from-Database/English-timed"
From Script | Spoken-Tutorial
Sandhya.np14 (Talk | contribs) |
Sandhya.np14 (Talk | contribs) |
||
| Line 117: | Line 117: | ||
|- | |- | ||
| 02:13 | | 02:13 | ||
| − | | So, type: | + | | So, type: "phenol" in the '''Input '''text-box. |
|- | |- | ||
| Line 125: | Line 125: | ||
|- | |- | ||
| 02:20 | | 02:20 | ||
| − | | A Model of | + | | A Model of phenol is displayed on the panel. |
|- | |- | ||
| Line 137: | Line 137: | ||
|- | |- | ||
| 02:36 | | 02:36 | ||
| − | | We can add substituents to the | + | | We can add substituents to the benzene '''ring''' of phenol. |
|- | |- | ||
| Line 185: | Line 185: | ||
|- | |- | ||
| 03:42 | | 03:42 | ||
| − | | For example '''cholesterol.''' | + | | For example: '''cholesterol.''' |
|- | |- | ||
| Line 193: | Line 193: | ||
|- | |- | ||
| 03:47 | | 03:47 | ||
| − | | Click on '''Get Mol''' option | + | | Click on '''Get Mol''' option. In the text-box, type: '''Cholesterol '''. |
|- | |- | ||
| Line 201: | Line 201: | ||
|- | |- | ||
| 03:57 | | 03:57 | ||
| − | | A molecule of '''Cholesterol '''is displayed on the | + | | A molecule of '''Cholesterol '''is displayed on the panel. |
|- | |- | ||
| Line 209: | Line 209: | ||
|- | |- | ||
| 04:08 | | 04:08 | ||
| − | | To highlight double-bond, | + | | To highlight double-bond, let us first change the color of '''carbon''' atoms of the double-bond. |
|- | |- | ||
| 04:15 | | 04:15 | ||
| − | | Click on | + | | Click on '''Select atoms''' icon in the tool bar. |
|- | |- | ||
| Line 233: | Line 233: | ||
|- | |- | ||
| 04:37 | | 04:37 | ||
| − | | Now | + | | Now click on ''' “Rotate molecule”''' option in the tool bar. |
|- | |- | ||
| Line 257: | Line 257: | ||
|- | |- | ||
| 05:08 | | 05:08 | ||
| − | | * Load structure of caffeine from '''Pubchem''' database . | + | | * '''Load''' structure of caffeine from '''Pubchem''' database. |
|- | |- | ||
| Line 273: | Line 273: | ||
|- | |- | ||
| 05:24 | | 05:24 | ||
| − | | We can convert '''2D structure'''s of molecules drawn in another software into '''3D model'''s. | + | | We can convert '''2D structure'''s of molecules, drawn in another software, into '''3D model'''s. |
|- | |- | ||
| Line 281: | Line 281: | ||
|- | |- | ||
| 05:36 | | 05:36 | ||
| − | | 2D structure of this molecule was drawn in software called '''GChemPaint.''' | + | | '''2D structure''' of this molecule was drawn in software called '''GChemPaint.''' |
|- | |- | ||
| 05:42 | | 05:42 | ||
| − | | The structure was saved as a | + | | The structure was saved as a ".mol" file. |
|- | |- | ||
| 05:46 | | 05:46 | ||
| − | | '''GchemPaint '''is an Open source software for drawing 2D chemical structures. | + | | '''GchemPaint '''is an '''Open source software''' for drawing '''2D''' chemical structures. |
|- | |- | ||
| Line 297: | Line 297: | ||
|- | |- | ||
| 05:56 | | 05:56 | ||
| − | | To draw structures and save | + | | To draw structures and '''save''' in ".mol" format, refer to '''Analysis of Compounds''' tutorial. |
|- | |- | ||
| 06:05 | | 06:05 | ||
| − | | Shown on this Gchempaint display area are 2D drawings of- | + | | Shown on this '''Gchempaint''' display area are 2D drawings of- |
|- | |- | ||
| Line 321: | Line 321: | ||
|- | |- | ||
| 06:24 | | 06:24 | ||
| − | | First | + | | First let's view the 2D structure of '''Alanine '''as 3D model, in '''Jmol Application'''. |
|- | |- | ||
| Line 333: | Line 333: | ||
|- | |- | ||
| 06:40 | | 06:40 | ||
| − | | I will choose '''Desktop''' folder and click on | + | | I will choose '''Desktop''' folder and click on '''Open'''. Choose the file 'Alanine.mol' and click on '''Open''' button. |
|- | |- | ||
| 06:51 | | 06:51 | ||
| − | | A 3D model of ''''Alanine'''' opens on screen. | + | | A '''3D model''' of ''''Alanine'''' opens on screen. |
|- | |- | ||
| Line 349: | Line 349: | ||
|- | |- | ||
| 07:08 | | 07:08 | ||
| − | | As with any '''.mol''' file, we can change the display using menu bar and also '''Pop-up '''menu. | + | | As with any '''".mol"''' file, we can change the display using menu bar and also '''Pop-up '''menu. |
|- | |- | ||
| Line 369: | Line 369: | ||
|- | |- | ||
| 07:32 | | 07:32 | ||
| − | | * Load chemical structures from '''Pubchem''' data base. | + | | * '''Load''' chemical structures from '''Pubchem''' data base. |
|- | |- | ||
| Line 405: | Line 405: | ||
|- | |- | ||
| 08:06 | | 08:06 | ||
| − | | # Save as | + | | # Save as '.mol' files. |
|- | |- | ||
| Line 414: | Line 414: | ||
| 08:12 | | 08:12 | ||
| Watch the video available at this URL. | | Watch the video available at this URL. | ||
| − | http://spoken-tutorial.org/ | + | http://spoken-tutorial.org/What_is_a_Spoken_Tutorial |
|- | |- | ||
| 08:16 | | 08:16 | ||
| − | | It summarizes the Spoken Tutorial project. | + | | It summarizes the '''Spoken Tutorial''' project. |
|- | |- | ||
| Line 430: | Line 430: | ||
|- | |- | ||
| 08:26 | | 08:26 | ||
| − | | Conducts workshops using spoken tutorials. | + | |* Conducts workshops using spoken tutorials. |
|- | |- | ||
| 08:29 | | 08:29 | ||
| − | | Gives certificates to those who pass an on-line test. | + | |* Gives certificates to those who pass an on-line test. |
|- | |- | ||
| 08:33 | | 08:33 | ||
| − | | For more details, please write to: | + | | For more details, please write to: |
| + | '''contact@spoken-tutorial.org''' | ||
|- | |- | ||
| Line 450: | Line 451: | ||
|- | |- | ||
| 08:52 | | 08:52 | ||
| − | | More information on this mission is available at this link: http://spoken-tutorial.org/NMEICT-Intro | + | | More information on this mission is available at this link: |
| + | http://spoken-tutorial.org/NMEICT-Intro | ||
|- | |- | ||
Revision as of 15:19, 11 February 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. |
