Jmol-Application/C2/Structures-from-Database/English-timed
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Revision as of 12:17, 20 October 2014 by PoojaMoolya (Talk | contribs)
Time | Narration |
00:01 | Welcome to this tutorial on Structures from Databases 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 data base '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.
ttp://spoken-tutorial.org/What_is_a_Spoken_ Tutorial |
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: |
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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 http://spoken-tutorial.org/NMEICT-Intro ] |
08:57 | This is Snehalatha from IIT Bombay signing off. Thank you for joining. |