Difference between revisions of "Jmol-Application/C2/Overview-of-Jmol-Application/English-timed"

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{| Border = 1
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! <center>Time</center>
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{|border=1
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! <center>Narration</center>
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||'''Time'''
 +
||'''Narration'''
  
 
|-
 
|-
−
| 00:01
+
||00:01
−
| Welcome to this Overview tutorial on '''Jmol Application''' series.
+
|| Welcome to this tutorial on '''Overview of''' '''Jmol Application'''.
  
 
|-
 
|-
−
| 00:06
+
||00:06
−
| In this tutorial we will go through,  
+
|| In this tutorial we will learn,  
 +
 
 +
About '''Jmol Application'''.
  
 
|-
 
|-
−
| 00:09
+
||00:12
−
|Important features of '''Jmol Application'''.
+
|| Download and run '''Jmol Application''' on '''Linux Operating System'''.
  
 
|-
 
|-
−
| 00:12
+
||00:18
−
|Information regarding download and installation on various operating systems.
+
|| Uses and advantages.
  
 
|-
 
|-
−
| 00:18
+
||00:21
−
|Uses of '''Jmol Application'''.
+
|| Play video clippings of '''Jmol Application''' tutorials available on our website.
  
 
|-
 
|-
−
| 00:21
+
|| 00:28
−
|We will Play clippings of video tutorials available in '''Jmol Application''' series at our website.
+
|| To record this tutorial, I am using,
 +
 
 +
'''Ubuntu Linux''' OS version 14.04
  
 
|-
 
|-
−
| 00:29
+
||00:35
−
|  To follow this tutorial you should have knowledge of, High School chemistry Or Basic Organic Chemistry
+
||  '''Java '''(JVM) version 1. 8
  
 
|-
 
|-
−
| 00:37
+
||00:38
−
|  To record this tutorial, I am using, '''Ubuntu '''OS version 12.10
+
||  '''Firefox web browser''' 54.0 and  A working''' internet''' connection
  
 
|-
 
|-
−
| 00:43
+
||00:45
−
|'''Jmol''' version 14.1.11
+
|| To follow this tutorial you should have knowledge of high school chemistry.
  
−
'''Java''' version 7
+
|-
 +
|| 00:50
 +
|| About '''Jmol Application'''.
  
−
and '''Mozilla Firefox Browser 35.0'''
+
'''Jmol''' is an open source '''3D viewer''' for:  Chemical structures, Biomolecules, Crystal structures and  Materials.
  
 
|-
 
|-
−
| 00:53
+
||01:02
−
| About '''Jmol Application''',
+
|| It runs on '''Windows, Mac, Linux''' operating systems and '''Android''' devices.
−
'''Jmol''' is a molecular viewer for three-dimensional chemical structures and macromolecules.
+
  
 +
|-
 +
|| 01:09
 +
|| It can be used to create and edit models of chemical structures.
  
 
|-
 
|-
−
| 01:02
+
||01:15
−
|'''Jmol''' can be used to create and edit 3D models of chemical structures.
+
|| '''Jmol''' is used by students, educators, and researchers in the fields of '''Chemistry''' and '''Biochemistry'''.
  
 
|-
 
|-
−
| 01:08
+
|| 01:23
−
|This software can be used by students, educators, and researchers in chemistry and biochemistry.
+
|| Here is the official website address for '''Jmol Application'''.
  
 
|-
 
|-
−
| 01:16
+
||01:28
−
| Here are some important features of '''Jmol.'''
+
|| Open this link in any '''web browser'''.
 +
 
 +
A web-page opens.
  
 
|-
 
|-
−
| 01:19
+
|| 01:35
−
|It is a Free and Open Source Software.
+
|| At the top-right corner of the page we see links for
 +
 
 +
'''Demonstration pages''',  '''Documentation''',  '''Wiki''',  '''Download''' and others
  
 
|-
 
|-
−
| 01:22
+
|| 01:48
−
|Works on '''Windows, Mac Operating System, Linux''' and also on '''android devices.'''
+
|| To download '''Jmol Application''', click on the '''Download''' link.
  
 
|-
 
|-
−
| 01:30
+
|| 01:53
−
|It supports all major web browsers.
+
|| The '''Download''' page opens with headings:
  
 
|-
 
|-
−
| 01:33
+
||01:57
−
|No special hardware is required for high quality 3D-rendering.
+
|| Scroll down to see the details.
 +
 
 +
 
 +
'''Downloading Jmol'''
  
 
|-
 
|-
−
| 01:38
+
||02:02
−
| Images can be exported to various file formats: Such as ''' jpg, png, gif, pdf ''' etc.
+
|| '''Requirements'''
  
 
|-
 
|-
−
| 01:47
+
||02:04
−
|Reads various file formats such as '''pdb, cif, mol, cml, xyz '''etc
+
|| '''Installing and running Jmol '''
  
 
|-
 
|-
−
| 01:56
+
||02:08
−
|If you are connected to internet you can directly loads models on '''Jmol''' panel:
+
|| '''Subversion Access'''
  
 
|-
 
|-
−
| 02:02
+
||02:11
−
|From databases such as '''pubchem''' for chemical structures.  
+
|| Scroll up to the '''Requirements''' section.
  
 
|-
 
|-
−
| 02:07
+
||02:14
−
|And '''PDB''' database for proteins and macromolecules.
+
|| Please note - standalone '''Jmol Application''' requires '''Java''' 1.4 or higher.  
  
 
|-
 
|-
−
| 02:12
+
|| 02:21
−
| More information about this software is available at the following links.  
+
|| If you do not have '''Java''' installed on your system, click on the '''link''' provided here.
  
 +
Follow the instructions.
  
 
|-
 
|-
−
| 02:18
+
|| 02:30
−
| Uses of '''Jmol''' :
+
|| Also read instructions for '''Installing and Running Jmol.'''
  
−
'''Jmol''' can be used as a teaching tool to explain concepts in chemistry.
+
|-
 +
|| 02:36
 +
|| Scroll up the page.
 +
Under the heading '''Downloading Jmol, '''click on '''download link.'''
  
 
|-
 
|-
−
| 02:26
+
|| 02:44
−
|And for producing high quality '''3D''' images that can be used in print media:
+
|| A new page opens.
−
such as journals, publications and books.
+
 
 +
A '''prompt''' appears that says download will start in a few seconds.
  
 
|-
 
|-
−
| 02:36
+
|| 02:53
−
|And also for presentations in classrooms and lectures.
+
|| After this, a dialog box appears which prompts you to save the file.  
  
 
|-
 
|-
−
| 02:41
+
||02:59
−
| Jmol can also be used for molecular modelling and producing animation movies.
+
|| Click on '''Save file '''option.
 +
 
 +
Then click on '''OK''' button.
  
 
|-
 
|-
−
| 02:48
+
|| 03:05
−
| Here is the webpage that describes how to incorporate '''Jmol''' images in powerpoint presentations.
+
|| Depending on the '''Internet''' speed, It may take a few minutes to complete the download.  
  
 
|-
 
|-
−
| 02:56
+
|| 03:12
−
| '''Jmol''' can be effectively used to teach certain topics in chemistry which require 3D visualization.
+
|| '''Jmol binary.zip file '''gets downloaded to the''' Downloads '''directory.  
  
 
|-
 
|-
−
| 03:03
+
|| 03:18
−
|At Basic level, topics such as: Structure and functional groups.  
+
|| Go to the directory where you have downloaded the file. Then extract the contents of the folder.
  
 
|-
 
|-
−
| 03:08
+
||03:25
−
|Atomic and Molecular orbitals.
+
|| Right-click on the '''zip''' file, from the context menu select '''Extract Here'''.
  
 
|-
 
|-
−
| 03:11
+
|| 03:33
−
| At advanced levels Jmol can be used to teach topics such as '''Stereochemistry''' which involves the study of spatial arrangement of atoms in a molecule.
+
|| Double-click on the extracted folder to open it.
 +
 
 +
Scroll down and find Jmol.jar file.
  
 
|-
 
|-
−
| 03:22
+
|| 03:42
−
|Symmetry and point-groups. Crystal Structure and Unit cell.
+
|| For '''Windows''' and '''Mac''', double-click on '''Jmol.jar''' file to open the '''Jmol''' interface.
  
 
|-
 
|-
−
| 03:27
+
|| 03:50
−
|And Predict proton NMR spectrum for molecules.  
+
|| I am using '''Ubuntu Linux''' operating system.
 +
 
 +
I will show how to run '''Jmol Application''' on my system.
  
 
|-
 
|-
−
| 03:31
+
|| 03:59
−
|This feature available in Jmol version 14.0 and above.
+
|| Right-click on '''Jmol.jar''' file. A '''context menu''' opens with options.
  
 
|-
 
|-
−
| 03:36
+
||04:07
−
|Jmol can be used to study Structure Activity Relationships.
+
|| I have already installed '''Java 8 Runtime Environment''' on my system.
  
 
|-
 
|-
−
| 03:41
+
||04:13
−
| Lets see how to download and install Jmol.
+
|| Fom the options in the context menu, I will select '''Open with Oracle Java 8 Runtime'''.
 +
 
 +
'''Jmol Application''' interface opens.
  
 
|-
 
|-
−
| 03:44
+
|| 04:25
−
|Jmol can be installed on '''Windows, Mac''' operating system and on '''Linux''' systems.
+
|| Another method to open '''Jmol''' interface is through '''terminal'''.
  
 
|-
 
|-
−
| 03:51
+
|| 04:30
−
|A special version of Jmol for Android devices is available at the link shown below.  
+
|| Open the '''terminal''' by pressing '''Ctrl, Alt''' and '''T''' keys simultaneously.
  
 
|-
 
|-
−
| 03:57
+
|| 04:36
−
| For Linux operating systems, download using Ubuntu software center or Synaptic package manager.
+
|| Navigate to '''Jmol''' folder which we had downloaded and extracted earlier.
  
 
|-
 
|-
−
| 04:04
+
||04:42
−
|Follow this tutorial in the linux series on our website.
+
|| To do so, at the '''prompt''' type '''cd space Downloads''', press '''Enter'''.
  
 
|-
 
|-
−
| 04:08
+
||04:50
−
| For '''Windows''' and '''Mac''' operating systems: Open the given link in any web browser.
+
|| Then type '''cd''' space and the name of the '''Jmol''' folder.  
  
 
|-
 
|-
−
| 04:15
+
||04:56
−
|I will open this link and quickly go through the contents given on the web-page.
+
|| In my case, it is '''Jmol hyphen fourteen dot twenty-nine dot four two'''
  
 
|-
 
|-
−
| 04:20
+
||05:03
−
| This web-page gives a lot of general information about Jmol. Scroll down the page.
+
|| You may have a different name depending on the version you have downloaded.
 +
 
 +
Press '''Enter'''.
  
 
|-
 
|-
−
| 04:27
+
|| 05:10
−
| It gives information about the overview, demonstration pages, features.
+
|| Then type '''java space hyphen jar space Jmol.jar'''
 +
 
 +
Press '''Enter'''.
  
 
|-
 
|-
−
| 04:35
+
||05:19
−
|To download Jmol click on the downloads page. Follow the instructions given on the page to download.
+
|| '''Jmol Application''' interface opens.
  
 
|-
 
|-
−
| 04:44
+
||05:24
−
|Information about installing and running Jmol is also given on this page.  
+
|| '''Linux''' users can also install '''Jmol''' using '''Ubuntu Software Center '''or''' Synaptic Package Manager.'''
  
 
|-
 
|-
−
| 04:50
+
||05:32
−
| I have created a series of tutorials which describe how to use this software.
+
|| For information on how to use these, please see the '''Linux''' series on this website.
  
 
|-
 
|-
−
| 04:56
+
|| 05:39
−
| The first tutorial '''Introduction to Jmol Application''' has information regarding the various features available on '''Jmol''' window.  
+
|| Back to '''Jmol''' interface.
 +
 
 +
Many features of '''Jmol''' are available in the menus on the menu bar and the toolbar.  
  
 
|-
 
|-
−
| 05:04
+
|| 05:52
−
|Here is the video clipping of that video.
+
|| Click on '''Help''' menu.  
  
 
|-
 
|-
−
|05:07
+
||05:54
−
|--------Add  Video clip ........
+
|| Here we have link for''' Jmol Wiki '''main page.
 +
 
 +
Click on '''Jmol Wiki'''.  
  
 
|-
 
|-
−
| 05:13
+
||06:02
−
| To create and edit molecular models, follow the tutorial '''Create and Edit'''.
+
|| If you are connected to the internet '''Jmol Wiki '''main page opens in the '''web browser'''.
−
Here is the clipping.
+
  
 
|-
 
|-
−
|05:18
+
|| 06:08
−
| ---- Add Video Clip------
+
|| This page has detailed information about '''Jmol''' and '''Jsmol'''.
  
 
|-
 
|-
−
| 05:27
+
||06:14
−
| We can Measure bond lengths, bond angles and dihedral angles.  Here is the video clipping.
+
|| '''JSmol''' is a '''Java''' independent version of '''Jmol.'''
  
 
|-
 
|-
−
|05:34
+
||06:19
−
|------- Add Vidoe clip-----
+
|| It runs in any '''HTML5 web browser'''.
  
 
|-
 
|-
−
|  05:40
+
|| 06:24
−
|  Using '''Jmol''' we can show surfaces and create atomic and molecular orbitals.
+
|| This page has links to various pages on the left panel.
 +
 
 +
|-
 +
||06:29
 +
|| The page also has various sections for topics such as
 +
 
 +
'''About Jmol and JSmol''', '''Installation''',  '''Development''' etc.
 +
 
 +
|-
 +
|| 06:40
 +
|| The section for '''Jmol Community''' has links to
 +
 
 +
'''Community and Users''' and '''Communities'''.
 +
 
 +
|-
 +
||06:47
 +
|| Click on '''Community and Users''' link.
 +
 
 +
|-
 +
|| 06:51
 +
|| '''Community''' page opens.
 +
 
 +
|-
 +
||06:54
 +
|| On this page you will find the work description of group of '''Jmol''' developers and '''Jmol''' users.
 +
 
 +
|-
 +
|| 07:02
 +
|| Different web pages for various '''sub-communities''' are available here.
 +
 
 +
I will click on '''Crystal community'''.
 +
 
 +
|-
 +
||07:10
 +
|| Here '''Jmol''' users can discuss their experiences in using '''Jmol''' for displaying crystal structures.
 +
 
 +
|-
 +
||07:19
 +
|| Please explore these pages according to your interest.
 +
 
 +
|-
 +
|| 07:25
 +
|| Advantages of '''Jmol Application.'''
 +
 
 +
No special hardware is required for high quality 3D-rendering.
 +
 
 +
|-
 +
||07:35
 +
||  If you are connected to internet you can directly load models on '''Jmol '''panel from
 +
 
 +
'''PubChem''' and '''PDB databases'''.
 +
 
 +
|-
 +
||07:44
 +
|| '''Jmol''' can be effectively used to teach certain topics in Chemistry.
 +
 
 +
|-
 +
||07:49
 +
|| For example: Structure and functional groups.
 +
 
 +
|-
 +
||07:53
 +
||  Atomic and Molecular orbitals.
 +
 
 +
|-
 +
||07:56
 +
|| Stereochemistry
 +
 
 +
|-
 +
||07:58
 +
|| Symmetry and point-groups.
 +
 
 +
|-
 +
||08:01
 +
|| Crystal structure and Unit cell.
 +
 
 +
|-
 +
|| 08:04
 +
||High quality 3D images can be produced, they can be used in publications and presentations
 +
 
 +
|-
 +
||08:13
 +
||View simulated '''proton and carbon 13 NMR spectra '''for molecules.
 +
 
 +
|-
 +
||08:19
 +
||  This feature is available in '''Jmol '''version 14.0 and above.
 +
 
 +
|-
 +
|| 08:25
 +
|| '''Jmol''' can also be used to study
 +
 
 +
Structure Activity Relationships
 +
 
 +
|-
 +
||08:31
 +
||  Molecular modelling
 +
 +
and Animation of molecules
 +
 
 +
|-
 +
|| 08:36
 +
|| We have created a series of tutorials which describe how to use this software.
 +
 
 +
|-
 +
||08:42
 +
|| The first tutorial is '''Introduction to Jmol Application'''.
 +
 
 +
|-
 +
||08:47
 +
|| It explains various features available on '''Jmol '''window.
 +
 
 +
|-
 +
||08:52
 +
||Create models of simple organic molecules.
 +
 
 +
Energy minimization and Save image.
 +
 
 +
|-
 +
||09:01
 +
|| Here is the video clipping.
 +
 
 +
|-
 +
||
 +
|| -----Add the audio----
 +
 
 +
|-
 +
||09:21
 +
|| Next tutorial '''Create and Edit Molecular Models''' explains how to
 +
 
 +
Add functional group
 +
 
 +
|-
 +
||09:29
 +
||  Add and delete atoms and bonds.
 +
 
 +
|-
 +
||09:32
 +
||Pop-up-menu.
 +
 
 +
|-
 +
||09:33
 +
|| Here is the video clipping.
 +
 
 +
|-
 +
||09:37
 +
|| ----Add the audio-----
 +
 
 +
|-
 +
|| 09:51
 +
|| Next tutorial '''Modify Display and View '''explains,
 +
 
 +
How to, modify the view.
 +
 
 +
|-
 +
||09:59
 +
||  Change the style of the display.
 +
 
 +
|-
 +
||10:02
 +
||  Save the image in various file formats.
 +
 
 
Here is the video clipping.
 
Here is the video clipping.
  
 
|-
 
|-
−
| 05:47
+
||
−
|-------- Add Video clip-------
+
||-----Add the audio------  
  
 
|-
 
|-
−
| 05:56
+
||10:28
−
| This video explains how to show Plane of symmetry and point-groups.
+
|| '''Next tutorial Measurements and Labeling''' tutorial explains,
 +
 
 +
|-
 +
||10:33
 +
||  How to measure bond lengths, bond angles and dihedral angles for a model.
 +
 
 +
|-
 +
||10:39
 +
|| Label atoms with symbols and number.
 +
 
 
Here is the video clipping.
 
Here is the video clipping.
  
 
|-
 
|-
−
| 06:02
+
||
−
|------------ Add Video clip-----------
+
|| -----Add the audio-----
  
 
|-
 
|-
−
| 06:09
+
|| 11:04
−
| Crystal structures and unit cell can be viewed using '''Jmol.''' Here is the video clipping.
+
|| Next tutorial '''Script Console and Script Commands''' explains
 +
 
 +
How to use script console and write script commands.
  
 
|-
 
|-
−
| 06:17
+
||11:14
−
|----------- Add Video clip --------------
+
|| Here is the video clipping.
  
 
|-
 
|-
−
| 06:24
+
||11:34
−
| Here is the video clipping to show proteins and macromolecules in Jmol.
+
|| Next tutorial '''Surfaces and Orbitals '''demonstrates how to-
 +
 
 +
Show surfaces, create models of aromatic molecules, atomic orbitals and molecular orbitals.
  
 
|-
 
|-
−
| 06:29
+
||11:46
−
|--------------- Add video clip-----------
+
|| Here is the video clipping.
  
 
|-
 
|-
−
| 06:37
+
||11:49
−
| A simulated H NMR spectrum can be displayed for all the molecules listed in chemical structure database: Starting from '''Jmol''' version 14.0
+
|| ------Add the audio------
  
 
|-
 
|-
−
| 06:49
+
|| 12:02
−
|Let me open '''Jmol''' window and demonstrate this feature.
+
|| Next tutorial '''Structures from Database '''explains-
 +
 
 +
How to load structures directly from chemical structure database such as '''PubChem'''.  
  
 
|-
 
|-
−
| 06:54
+
||12:13
−
|  To view simulated proton NMR: Go to tools menu.
+
||  Convert 2D structures drawn in GChemPaint to 3D models in Jmol
 +
 
 +
Here is the video clipping.
  
 
|-
 
|-
−
| 06:59
+
||
−
|Scroll down to '''spectra''' and click on '''spectrum'''
+
|| -----Add the audio------
  
 
|-
 
|-
−
| 07:04
+
||12:42
−
|The '''Jspecview''' window opens.  
+
|| Next tutorial '''Crystal structure and Unit Cell '''shows demonstration of-
 +
 
 +
Download and open '''CIF''' files in Jmol.
  
 
|-
 
|-
−
| 07:08
+
||12:52
−
|Scroll down the file menu, click on '''add simulation'''
+
||  Display '''unit cell''' and '''unit cell''' parameters.
  
 
|-
 
|-
−
| 07:13
+
||12:56
−
|In the dialog box enter the name of the molecule.
+
||  Display crystal structures of different crystal systems.
 +
 
 +
Here is the video clipping.
  
 
|-
 
|-
−
| 07:17
+
||
−
|Let us type '''nitrobenzene''', click on ok button.
+
|| ----Add the audio-----
  
 
|-
 
|-
−
| 07:22
+
|| 13:20
−
|A proton NMR spectrum of nitrobenzene is displayed on the panel.
+
|| Next tutorial,''' Proteins and macromolecules '''tutorial demonstrates how to
 +
 
 +
Download '''pdb''' files from database.
  
 
|-
 
|-
−
| 07:28
+
||13:29
−
|Atoms on the structure are correlated with signals in the spectrum.
+
||  View and modify secondary structure of a protein.
 +
 
 +
Here is the video clipping of this tutorial.  
  
 
|-
 
|-
−
| 07:33
+
||
−
| Certain files include information about molecular vibrations, such as '''GAMESS .log files''' and Spartan output files.'''
+
|| ---Add the Audio----
  
 
|-
 
|-
−
| 07:45
+
|| 13:52
−
|We can open these files in '''Jmol''' and view vibrations.
+
|| Next tutorial '''3D Models of Enzymes''' explains how to-
 +
 
 +
Modify the display of secondary structure.
  
 
|-
 
|-
−
| 07:50
+
||14:00
−
|  Let me open a log file showing vibrations in '''carbondioxide ''' molecule.
+
||  Highlight amino acid residues and substrate.
  
 
|-
 
|-
−
| 08:00
+
||14:04
−
|  Here is an animation, showing vibrations in '''benzene''' molecule.
+
||  View '''Ramachandran''' plot for proteins.
  
 
|-
 
|-
−
| 08:05
+
||14:08
−
| Here is the animation showing conformations in '''cyclohexane''' molecule.
+
|| Here is the video clipping.  
  
 
|-
 
|-
−
| 08:15
+
||
−
| Let us summarize, In this tutorial we have learnt,
+
|| -----Add the audio-----
  
 
|-
 
|-
−
| 08:19
+
|| 14:22
−
|Important features of '''Jmol Application'''.
+
|| Next tutorial '''Symmetry and Point Groups '''demonstrates
  
 
|-
 
|-
−
| 08:22
+
||14:27
−
|Information regarding Installation on various operating systems.
+
||  C2 and C3 rotational axes, reflection planes and point group classification.
  
−
Uses of '''Jmol Application'''.
+
Here is the video clipping
  
 
|-
 
|-
−
| 08:29
+
|| 14:51
−
| We have also seen clippings of video tutorials in '''Jmol Application''' series.
+
|| Next tutorial '''Animation using Script Commands''' demonstrates
 +
 
 +
Animation using '''script commands'''. Save the animation as '''GIF''' file.
 +
 
 +
|-
 +
||15:02
 +
|| Here is the video clipping
 +
 
 +
|-
 +
||
 +
|| ----Add the Audio--------
 +
 
 +
|-
 +
|| 15:23
 +
|| Let us summarize,
 +
 
 +
In this tutorial we have learnt, About Jmol Application.
 +
 
 +
|-
 +
||15:30
 +
|| Download and run Jmol Application on Linux OS.
 +
 
 +
Uses and advantages.
 +
 
 +
|-
 +
||15:38
 +
||Play video clippings of Jmol Application tutorials available on our website.
 +
 
 +
|-
 +
|| 15:44
 +
|| As an assignment- Explore Jmol Application interface.
 +
 
 +
|-
 +
||15:50
 +
|| On the '''Jmol Wiki''' main page, explore '''Jmol Documentation''' page.
 +
 
 +
|-
 +
|| 15:56
 +
|| The video at the following link summarizes the Spoken Tutorial project.
 +
 
 +
Please download and watch it.
 +
 
 +
|-
 +
|| 16:04
 +
|| The '''Spoken Tutorial Project '''team: conducts workshops using spoken tutorials and
 +
 
 +
gives certificates on passing online tests.
 +
 
 +
|-
 +
||16:12
 +
|| For more details, please write to us.
 +
 
 +
|-
 +
|| 16:15
 +
|| Do you have questions in THIS Spoken Tutorial?
 +
 
 +
Please visit this site.
 +
 
 +
|-
 +
||16:21
 +
||  Choose the minute and second where you have the question.
 +
 
 +
Explain your question briefly.
  
 
|-
 
|-
−
| 08:35
+
||16:28
−
|And some animation videos showing vibrations and conformations of '''cyclohexane.'''
+
|| Someone from our team will answer them.
  
 
|-
 
|-
−
| 08:42
+
|| 16:30
−
| The video at the following link summarizes the Spoken Tutorial project.  
+
|| The Spoken Tutorial forum is for specific questions on this tutorial.
  
−
Please download and watch it.  
+
Please do not post unrelated and general questions on them.
  
 
|-
 
|-
−
| 08:48
+
||16:42
−
|  The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.  
+
||  This will help reduce the clutter.
  
−
For more details, please write to us.  
+
With less clutter, we can use this discussion as instructional material.
  
 
|-
 
|-
−
| 08:59
+
||16:51
−
| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.  
+
|| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
  
−
More information on this Mission is available at the link shown.  
+
More information on this mission is available at this link.
  
 
|-
 
|-
−
|09:09
+
|| 17:02
−
| This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
+
|| This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
  
 
|}
 
|}

Latest revision as of 12:18, 7 August 2019

Time Narration
00:01 Welcome to this tutorial on Overview of Jmol Application.
00:06 In this tutorial we will learn,

About Jmol Application.

00:12 Download and run Jmol Application on Linux Operating System.
00:18 Uses and advantages.
00:21 Play video clippings of Jmol Application tutorials available on our website.
00:28 To record this tutorial, I am using,

Ubuntu Linux OS version 14.04

00:35 Java (JVM) version 1. 8
00:38 Firefox web browser 54.0 and A working internet connection
00:45 To follow this tutorial you should have knowledge of high school chemistry.
00:50 About Jmol Application.

Jmol is an open source 3D viewer for: Chemical structures, Biomolecules, Crystal structures and Materials.

01:02 It runs on Windows, Mac, Linux operating systems and Android devices.
01:09 It can be used to create and edit models of chemical structures.
01:15 Jmol is used by students, educators, and researchers in the fields of Chemistry and Biochemistry.
01:23 Here is the official website address for Jmol Application.
01:28 Open this link in any web browser.

A web-page opens.

01:35 At the top-right corner of the page we see links for

Demonstration pages, Documentation, Wiki, Download and others

01:48 To download Jmol Application, click on the Download link.
01:53 The Download page opens with headings:
01:57 Scroll down to see the details.


Downloading Jmol

02:02 Requirements
02:04 Installing and running Jmol
02:08 Subversion Access
02:11 Scroll up to the Requirements section.
02:14 Please note - standalone Jmol Application requires Java 1.4 or higher.
02:21 If you do not have Java installed on your system, click on the link provided here.

Follow the instructions.

02:30 Also read instructions for Installing and Running Jmol.
02:36 Scroll up the page.

Under the heading Downloading Jmol, click on download link.

02:44 A new page opens.

A prompt appears that says download will start in a few seconds.

02:53 After this, a dialog box appears which prompts you to save the file.
02:59 Click on Save file option.

Then click on OK button.

03:05 Depending on the Internet speed, It may take a few minutes to complete the download.
03:12 Jmol binary.zip file gets downloaded to the Downloads directory.
03:18 Go to the directory where you have downloaded the file. Then extract the contents of the folder.
03:25 Right-click on the zip file, from the context menu select Extract Here.
03:33 Double-click on the extracted folder to open it.

Scroll down and find Jmol.jar file.

03:42 For Windows and Mac, double-click on Jmol.jar file to open the Jmol interface.
03:50 I am using Ubuntu Linux operating system.

I will show how to run Jmol Application on my system.

03:59 Right-click on Jmol.jar file. A context menu opens with options.
04:07 I have already installed Java 8 Runtime Environment on my system.
04:13 Fom the options in the context menu, I will select Open with Oracle Java 8 Runtime.

Jmol Application interface opens.

04:25 Another method to open Jmol interface is through terminal.
04:30 Open the terminal by pressing Ctrl, Alt and T keys simultaneously.
04:36 Navigate to Jmol folder which we had downloaded and extracted earlier.
04:42 To do so, at the prompt type cd space Downloads, press Enter.
04:50 Then type cd space and the name of the Jmol folder.
04:56 In my case, it is Jmol hyphen fourteen dot twenty-nine dot four two
05:03 You may have a different name depending on the version you have downloaded.

Press Enter.

05:10 Then type java space hyphen jar space Jmol.jar

Press Enter.

05:19 Jmol Application interface opens.
05:24 Linux users can also install Jmol using Ubuntu Software Center or Synaptic Package Manager.
05:32 For information on how to use these, please see the Linux series on this website.
05:39 Back to Jmol interface.

Many features of Jmol are available in the menus on the menu bar and the toolbar.

05:52 Click on Help menu.
05:54 Here we have link for Jmol Wiki main page.

Click on Jmol Wiki.

06:02 If you are connected to the internet Jmol Wiki main page opens in the web browser.
06:08 This page has detailed information about Jmol and Jsmol.
06:14 JSmol is a Java independent version of Jmol.
06:19 It runs in any HTML5 web browser.
06:24 This page has links to various pages on the left panel.
06:29 The page also has various sections for topics such as

About Jmol and JSmol, Installation, Development etc.

06:40 The section for Jmol Community has links to

Community and Users and Communities.

06:47 Click on Community and Users link.
06:51 Community page opens.
06:54 On this page you will find the work description of group of Jmol developers and Jmol users.
07:02 Different web pages for various sub-communities are available here.

I will click on Crystal community.

07:10 Here Jmol users can discuss their experiences in using Jmol for displaying crystal structures.
07:19 Please explore these pages according to your interest.
07:25 Advantages of Jmol Application.

No special hardware is required for high quality 3D-rendering.

07:35 If you are connected to internet you can directly load models on Jmol panel from

PubChem and PDB databases.

07:44 Jmol can be effectively used to teach certain topics in Chemistry.
07:49 For example: Structure and functional groups.
07:53 Atomic and Molecular orbitals.
07:56 Stereochemistry
07:58 Symmetry and point-groups.
08:01 Crystal structure and Unit cell.
08:04 High quality 3D images can be produced, they can be used in publications and presentations
08:13 View simulated proton and carbon 13 NMR spectra for molecules.
08:19 This feature is available in Jmol version 14.0 and above.
08:25 Jmol can also be used to study

Structure Activity Relationships

08:31 Molecular modelling

and Animation of molecules

08:36 We have created a series of tutorials which describe how to use this software.
08:42 The first tutorial is Introduction to Jmol Application.
08:47 It explains various features available on Jmol window.
08:52 Create models of simple organic molecules.

Energy minimization and Save image.

09:01 Here is the video clipping.
-----Add the audio----
09:21 Next tutorial Create and Edit Molecular Models explains how to

Add functional group

09:29 Add and delete atoms and bonds.
09:32 Pop-up-menu.
09:33 Here is the video clipping.
09:37 ----Add the audio-----
09:51 Next tutorial Modify Display and View explains,

How to, modify the view.

09:59 Change the style of the display.
10:02 Save the image in various file formats.

Here is the video clipping.

-----Add the audio------
10:28 Next tutorial Measurements and Labeling tutorial explains,
10:33 How to measure bond lengths, bond angles and dihedral angles for a model.
10:39 Label atoms with symbols and number.

Here is the video clipping.

-----Add the audio-----
11:04 Next tutorial Script Console and Script Commands explains

How to use script console and write script commands.

11:14 Here is the video clipping.
11:34 Next tutorial Surfaces and Orbitals demonstrates how to-

Show surfaces, create models of aromatic molecules, atomic orbitals and molecular orbitals.

11:46 Here is the video clipping.
11:49 ------Add the audio------
12:02 Next tutorial Structures from Database explains-

How to load structures directly from chemical structure database such as PubChem.

12:13 Convert 2D structures drawn in GChemPaint to 3D models in Jmol

Here is the video clipping.

-----Add the audio------
12:42 Next tutorial Crystal structure and Unit Cell shows demonstration of-

Download and open CIF files in Jmol.

12:52 Display unit cell and unit cell parameters.
12:56 Display crystal structures of different crystal systems.

Here is the video clipping.

----Add the audio-----
13:20 Next tutorial, Proteins and macromolecules tutorial demonstrates how to

Download pdb files from database.

13:29 View and modify secondary structure of a protein.

Here is the video clipping of this tutorial.

---Add the Audio----
13:52 Next tutorial 3D Models of Enzymes explains how to-

Modify the display of secondary structure.

14:00 Highlight amino acid residues and substrate.
14:04 View Ramachandran plot for proteins.
14:08 Here is the video clipping.
-----Add the audio-----
14:22 Next tutorial Symmetry and Point Groups demonstrates
14:27 C2 and C3 rotational axes, reflection planes and point group classification.

Here is the video clipping

14:51 Next tutorial Animation using Script Commands demonstrates

Animation using script commands. Save the animation as GIF file.

15:02 Here is the video clipping
----Add the Audio--------
15:23 Let us summarize,

In this tutorial we have learnt, About Jmol Application.

15:30 Download and run Jmol Application on Linux OS.

Uses and advantages.

15:38 Play video clippings of Jmol Application tutorials available on our website.
15:44 As an assignment- Explore Jmol Application interface.
15:50 On the Jmol Wiki main page, explore Jmol Documentation page.
15:56 The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

16:04 The Spoken Tutorial Project team: conducts workshops using spoken tutorials and

gives certificates on passing online tests.

16:12 For more details, please write to us.
16:15 Do you have questions in THIS Spoken Tutorial?

Please visit this site.

16:21 Choose the minute and second where you have the question.

Explain your question briefly.

16:28 Someone from our team will answer them.
16:30 The Spoken Tutorial forum is for specific questions on this tutorial.

Please do not post unrelated and general questions on them.

16:42 This will help reduce the clutter.

With less clutter, we can use this discussion as instructional material.

16:51 Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this mission is available at this link.

17:02 This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14

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