Difference between revisions of "Jmol-Application/C2/Structures-from-Database/English-timed"
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− | | Welcome to this tutorial on '''Structures from | + | | Welcome to this tutorial on '''Structures from Database''' in '''Jmol''' |
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| 00:07 | | 00:07 | ||
− | | In this tutorial, we will learn to | + | | In this tutorial, we will learn to: |
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| 00:10 | | 00:10 | ||
− | | * Load chemical structures from '''PubChem''' database and | + | | * '''Load''' chemical structures from '''PubChem''' database and |
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| 00:21 | | 00:21 | ||
− | | To follow this tutorial you should be familiar with '''Jmol Application'''. | + | | To follow this tutorial, you should be familiar with '''Jmol Application'''. |
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| 00:33 | | 00:33 | ||
− | | To record this tutorial I am using | + | | To record this tutorial, I am using: |
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|00:44 | |00:44 | ||
− | | * '''Java''' version 7 | + | | * '''Java''' version 7. |
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| 01:00 | | 01:00 | ||
− | | '''Jmol''' has a feature to load | + | | '''Jmol''' has a feature to '''load structure'''s of compounds listed in the '''database'''. |
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| 01:07 | | 01:07 | ||
− | | The ''''File'''' menu on the menu bar | + | | 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 | + | | This loads molecules from chemical structure database ''''PubChem'.''' |
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| 01:17 | | 01:17 | ||
− | | It also has another option ''''Get PDB'''' to load protein structures from '''Protein Data Bank'''. | + | | It also has another option ''''Get PDB'''' to load '''protein''' structures from '''Protein Data Bank'''. |
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| 01:36 | | 01:36 | ||
− | | An ''''Input'''' dialog box opens on the screen. | + | | An ''''Input'''' dialog box opens on the '''screen'''. |
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| 01:48 | | 01:48 | ||
− | | Common name or '''IUPAC''' name | + | | Common name or '''IUPAC''' name, |
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| 01:51 | | 01:51 | ||
− | | '''CAS '''number | + | | '''CAS '''number, |
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| 01:54 | | 01:54 | ||
− | | '''CID''' number | + | | '''CID''' number, |
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| 01:58 | | 01:58 | ||
− | |'''SMILES identifier''' | + | |'''SMILES identifier'''. |
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| 02:01 | | 02:01 | ||
− | | Please visit '''Pubchem''' database website for information on identification numbers for a particular chemical | + | | Please visit '''Pubchem''' database website for information on identification numbers for a particular chemical. |
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| 02:09 | | 02:09 | ||
− | | | + | | Let us display '''phenol''' on screen. |
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| 02:13 | | 02:13 | ||
− | | So type ''''phenol'''' in the '''Input '''text box. | + | | So, type: ''''phenol'''' in the '''Input '''text box. |
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|02:30 | |02:30 | ||
− | | These options are listed in the '''Menu bar '''and '''Pop | + | | These options are listed in the '''Menu bar '''and '''Pop-up''' menu. |
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| 02:41 | | 02:41 | ||
− | | First let us label the atoms in the model. | + | | First, let us label the atoms in the '''model'''. |
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| 02:45 | | 02:45 | ||
− | | Click on the ''' | + | | Click on the '''Display''' menu and select''' Label'''. Click on '''Number '''option. |
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| 02:52 | | 02:52 | ||
− | | Now, let's replace a '''hydrogen number 10 '''attached to the '''carbon atom number 4 '''with an | + | | Now, let's replace a '''hydrogen number 10 '''attached to the '''carbon atom number 4 '''with an '''amino group'''. |
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|03:00 | |03:00 | ||
− | | Open the '''modelkit | + | | Open the '''modelkit''' menu, select '''nitrogen''' from the options. |
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| 03:30 | | 03:30 | ||
− | | On the panel we have a model of '''Para-Amino-phenol''' in sticks display. | + | | On the panel, we have a model of '''Para-Amino-phenol''' in '''sticks''' display. |
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| 03:36 | | 03:36 | ||
− | | Complex structures | + | | Complex structures which are difficult to create, can easily be loaded on the '''panel'''. |
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| 03:45 | | 03:45 | ||
− | | Click on '''File''' menu | + | | Click on '''File''' menu. |
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| 03:47 | | 03:47 | ||
− | | Click on '''Get Mol''' option, in the text box type '''Cholesterol '''. | + | | Click on '''Get Mol''' option, in the text box type: '''Cholesterol '''. |
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| 04:02 | | 04:02 | ||
− | | We can highlight the features like '''double-bond''' and '''side-chain '''in the molecule | + | | We can highlight the features like '''double-bond''' and '''side-chain '''in the molecule. |
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| 05:06 | | 05:06 | ||
− | | As an assignment | + | | As an assignment- |
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| 05:24 | | 05:24 | ||
− | | We can convert 2D | + | | We can convert '''2D structure'''s of molecules drawn in another software into '''3D model'''s. |
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| 05:31 | | 05:31 | ||
− | | Here I have a model of '''aminoacid Alanine''' on the panel. | + | | Here, I have a model of '''aminoacid Alanine''' on the panel. |
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| 05:42 | | 05:42 | ||
− | | The structure was saved as a '''.mol '''file. | + | | The structure was saved as a ''''.mol' '''file. |
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| 05:56 | | 05:56 | ||
− | | To draw structures and save in .mol format, refer to Analysis of Compounds tutorial. | + | | To draw structures and save in '.mol' format, refer to '''Analysis of Compounds''' tutorial. |
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| 06:05 | | 06:05 | ||
− | | Shown on this Gchempaint display area are 2D drawings of | + | | Shown on this Gchempaint display area are 2D drawings of- |
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| 06:14 | | 06:14 | ||
− | | * '''Saccharide -Alpha-D glucopyranose''' | + | | * '''Saccharide -Alpha-D glucopyranose'''. |
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| 06:19 | | 06:19 | ||
− | | I have saved them in '''.mol '''format on my '''Desktop.''' | + | | I have saved them in ''''.mol'''' format on my '''Desktop.''' |
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| 06:36 | | 06:36 | ||
− | | Click on | + | | Click on '''Open a file''' icon in the tool bar. |
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| 06:55 | | 06:55 | ||
− | | Open the '''modelkit | + | | Open the '''modelkit''' menu and click on ''''fix hydrogens and minimize'''' option. |
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| 07:25 | | 07:25 | ||
− | | Let's summarize | + | | Let's summarize. |
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| 07:27 | | 07:27 | ||
− | | In this tutorial we have learnt to | + | | In this tutorial, we have learnt to: |
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| 07:56 | | 07:56 | ||
− | | # Draw 2D structures of the following '''Amino acids''' in '''GChemPaint | + | | # Draw 2D structures of the following '''Amino acids''' in '''GChemPaint'''- |
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| 08:06 | | 08:06 | ||
− | | # Save as '''.mol '''files. | + | | # Save as ''''.mol' '''files. |
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| 08:12 | | 08:12 | ||
| Watch the video available at this URL. | | Watch the video available at this URL. | ||
− | + | http://spoken-tutorial.org/What]_is_a_Spoken_Tutorial | |
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| 08:16 | | 08:16 | ||
− | | It summarizes the Spoken Tutorial project | + | | It summarizes the Spoken Tutorial project. |
|- | |- | ||
| 08:19 | | 08:19 | ||
− | | 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. |
|- | |- | ||
| 08:23 | | 08:23 | ||
− | |The Spoken Tutorial Project | + | |The Spoken Tutorial Project team: |
|- | |- | ||
| 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 contact@spoken-tutorial.org | + | | For more details, please write to: contact@spoken-tutorial.org |
|- | |- | ||
| 08:40 | | 08:40 | ||
− | | Spoken Tutorial | + | | '''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project. |
|- | |- | ||
| 08:45 | | 08:45 | ||
− | | 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. |
|- | |- | ||
| 08:52 | | 08:52 | ||
− | | More information on this | + | | More information on this mission is available at this link: http://spoken-tutorial.org/NMEICT-Intro |
|- | |- | ||
| 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. |
|} | |} |
Revision as of 14:37, 14 September 2015
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.
http://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: |
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: http://spoken-tutorial.org/NMEICT-Intro |
08:57 | This is Snehalatha from IIT Bombay, signing off. Thank you for joining. |