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

From Script | Spoken-Tutorial
Jump to: navigation, search
(Created page with "{| Border = 1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 | Welcome to this Overview tutorial on '''Jmol Application''' series. |- | 00:06 | In this t...")
 
Line 9: Line 9:
 
|-
 
|-
 
| 00:06
 
| 00:06
−
|  In this tutorial we will go through,
+
|  In this tutorial, we will go through:
  
 
|-
 
|-
 
| 00:09
 
| 00:09
−
|Important features of '''Jmol Application'''.
+
|* Important features of '''Jmol Application'''.
  
 
|-
 
|-
 
| 00:12
 
| 00:12
−
|Information regarding download and installation on various operating systems.
+
|* Information regarding download and installation on various operating systems.
  
 
|-
 
|-
 
| 00:18
 
| 00:18
−
|Uses of '''Jmol Application'''.
+
|* Uses of '''Jmol Application'''.
  
 
|-
 
|-
 
| 00:21
 
| 00:21
−
|We will Play clippings of video tutorials available in '''Jmol Application''' series at our website.
+
|We will play clippings of video tutorials available in '''Jmol Application''' series at our website.
  
 
|-
 
|-
 
| 00:29
 
| 00:29
−
|  To follow this tutorial you should have knowledge of, High School chemistry Or Basic Organic Chemistry
+
|  To follow this tutorial, you should have knowledge of High School chemistry Or Basic Organic Chemistry.
  
 
|-
 
|-
 
| 00:37
 
| 00:37
−
|  To record this tutorial, I am using, '''Ubuntu '''OS version 12.10
+
|  To record this tutorial, I am using:* '''Ubuntu '''OS version 12.10
  
 
|-
 
|-
 
| 00:43
 
| 00:43
−
|'''Jmol''' version 14.1.11
+
|* '''Jmol''' version 14.1.11
  
−
'''Java''' version 7
+
* '''Java''' version 7
  
−
and '''Mozilla Firefox Browser 35.0'''
+
and* '''Mozilla Firefox Browser 35.0'''
  
 
|-
 
|-
 
| 00:53
 
| 00:53
−
|  About '''Jmol Application''',
+
|  About '''Jmol Application''':
 
'''Jmol''' is a molecular viewer for three-dimensional chemical structures and macromolecules.
 
'''Jmol''' is a molecular viewer for three-dimensional chemical structures and macromolecules.
−
 
  
 
|-
 
|-
Line 55: Line 54:
 
|-
 
|-
 
| 01:08
 
| 01:08
−
|This software can be used by students, educators, and researchers in chemistry and biochemistry.
+
|This software can be used by students, educators and researchers in chemistry and biochemistry.
  
 
|-
 
|-
Line 79: Line 78:
 
|-
 
|-
 
| 01:38
 
| 01:38
−
|  Images can be exported to various file formats: Such as  ''' jpg, png, gif, pdf ''' etc.
+
|  Images can be exported to various file formats such as: '''jpg, png, gif, pdf''' etc.
  
 
|-
 
|-
 
| 01:47
 
| 01:47
−
|Reads various file formats such as '''pdb, cif, mol, cml, xyz '''etc
+
|Reads various file formats such as: '''pdb, cif, mol, cml, xyz '''etc.
  
 
|-
 
|-
 
| 01:56
 
| 01:56
−
|If you are connected to internet you can directly  loads models on '''Jmol''' panel:
+
|If you are connected to internet, you can directly  load models on '''Jmol''' panel:
  
 
|-
 
|-
Line 100: Line 99:
 
| 02:12
 
| 02:12
 
|  More information about this software is available at the following links.  
 
|  More information about this software is available at the following links.  
−
 
  
 
|-
 
|-
Line 110: Line 108:
 
|-
 
|-
 
| 02:26
 
| 02:26
−
|And for producing high quality '''3D''' images that can be used in print media:
+
|And for producing high quality '''3D''' images that can be used in print media such as journals, publications and books.
−
such as journals, publications and books.
+
  
 
|-
 
|-
Line 131: Line 128:
 
|-
 
|-
 
| 03:03
 
| 03:03
−
|At Basic level, topics such as: Structure and functional groups.  
+
|At Basic level, topics such as:* Structure and functional groups.  
  
 
|-
 
|-
 
| 03:08
 
| 03:08
−
|Atomic and Molecular orbitals.
+
|* Atomic and Molecular orbitals.
  
 
|-
 
|-
 
| 03:11
 
| 03:11
−
|  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.
+
|  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.
  
 
|-
 
|-
 
| 03:22
 
| 03:22
−
|Symmetry and point-groups. Crystal Structure and Unit cell.
+
|* Symmetry and point-groups. * Crystal Structure and Unit cell
  
 
|-
 
|-
Line 151: Line 148:
 
|-
 
|-
 
| 03:31
 
| 03:31
−
|This feature available in Jmol version 14.0 and above.
+
|This feature is available in Jmol version 14.0 and above.
  
 
|-
 
|-
Line 159: Line 156:
 
|-
 
|-
 
| 03:41
 
| 03:41
−
| Lets see how to download and install Jmol.
+
| Let's see how to download and install Jmol.
  
 
|-
 
|-
Line 171: Line 168:
 
|-
 
|-
 
|  03:57
 
|  03:57
−
| For Linux operating systems, download using Ubuntu software center or Synaptic package manager.
+
| For Linux operating systems, download using '''Ubuntu software center''' or '''Synaptic package manager'''.
  
 
|-
 
|-
Line 187: Line 184:
 
|-
 
|-
 
|  04:20
 
|  04:20
−
|  This web-page gives a lot of general information about Jmol. Scroll down the page.
+
|  This web-page gives a lot of general information about Jmol. Scroll-down the page.
  
 
|-
 
|-
Line 195: Line 192:
 
|-
 
|-
 
| 04:35
 
| 04:35
−
|To download Jmol click on the downloads page. Follow the instructions given on the page to download.
+
|To download Jmol, click on the '''downloads''' page. Follow the instructions given on the page to download.
  
 
|-
 
|-
 
| 04:44
 
| 04:44
−
|Information about installing and running Jmol is also given on this page.  
+
|Information about installing and '''run'''ning Jmol is also given on this page.  
  
 
|-
 
|-
Line 228: Line 225:
 
|-
 
|-
 
| 05:27
 
| 05:27
−
|  We can Measure bond lengths, bond angles and dihedral angles.  Here is the video clipping.
+
|  We can measure bond lengths, bond angles and dihedral angles.  Here is the video clipping.
  
 
|-
 
|-
Line 236: Line 233:
 
|-
 
|-
 
|  05:40
 
|  05:40
−
|  Using '''Jmol''' we can show surfaces and create atomic and molecular orbitals.
+
|  Using '''Jmol''', we can show surfaces and create atomic and molecular orbitals.
 
Here is the video clipping.
 
Here is the video clipping.
  
Line 282: Line 279:
 
|-
 
|-
 
| 06:59
 
| 06:59
−
|Scroll down to '''spectra''' and click on '''spectrum'''
+
|Scroll-down to '''Spectra''' and click on '''Spectrum'''.
  
 
|-
 
|-
Line 290: Line 287:
 
|-
 
|-
 
| 07:08
 
| 07:08
−
|Scroll down the file menu, click on '''add simulation'''
+
|Scroll-down the '''File''' menu, click on '''Add simulation'''.
  
 
|-
 
|-
 
| 07:13
 
| 07:13
−
|In the dialog box enter the name of the molecule.
+
|In the dialog-box, enter the name of the molecule.
  
 
|-
 
|-
 
| 07:17
 
| 07:17
−
|Let us type '''nitrobenzene''', click on ok button.  
+
|Let us type "nitrobenzene", click on '''OK''' button.  
  
 
|-
 
|-
Line 310: Line 307:
 
|-
 
|-
 
| 07:33
 
| 07:33
−
|  Certain files include information about molecular vibrations, such as '''GAMESS .log files''' and Spartan output files.'''
+
|  Certain files include information about molecular vibrations such as '''GAMESS .log files''' and '''Spartan output files.'''
  
 
|-
 
|-
Line 318: Line 315:
 
|-
 
|-
 
|  07:50
 
|  07:50
−
|  Let me open a log file showing vibrations in '''carbondioxide ''' molecule.
+
|  Let me open a '''log file''' showing vibrations in '''carbondioxide ''' molecule.
  
 
|-
 
|-
Line 330: Line 327:
 
|-
 
|-
 
| 08:15
 
| 08:15
−
|  Let us summarize, In this tutorial we have learnt,
+
|  Let us summarize. In this tutorial, we have learnt:
  
 
|-
 
|-
 
| 08:19
 
| 08:19
−
|Important features of '''Jmol Application'''.
+
|* Important features of '''Jmol Application'''
  
 
|-
 
|-
 
| 08:22
 
| 08:22
−
|Information regarding Installation on various operating systems.
+
|* Information regarding Installation on various operating systems
−
 
+
* Uses of '''Jmol Application'''.
−
Uses of '''Jmol Application'''.
+
  
 
|-
 
|-
 
| 08:29
 
| 08:29
−
| We have also seen clippings of video tutorials in '''Jmol Application''' series.
+
| We have also seen clippings of video tutorials in '''Jmol Application''' series.
  
 
|-
 
|-
 
| 08:35
 
| 08:35
−
|And some animation videos showing vibrations and conformations of '''cyclohexane.'''
+
|And, some animation videos showing vibrations and conformations of '''cyclohexane.'''
  
 
|-
 
|-
 
| 08:42
 
| 08:42
−
|  The video at the following link summarizes the Spoken Tutorial project.  
+
|  The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.  
−
 
+
−
Please download and watch it.  
+
  
 
|-
 
|-
 
| 08:48
 
| 08:48
−
|  The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.  
+
|  The Spoken Tutorial project team conducts workshops and gives certificates for those who pass an online test.  
−
 
+
 
For more details, please write to us.  
 
For more details, please write to us.  
  
 
|-
 
|-
 
| 08:59
 
| 08:59
−
|  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 the link shown.  
  
 
|-
 
|-
 
|09:09
 
|09:09
−
|  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 18:06, 3 February 2016

Time
Narration
00:01 Welcome to this Overview tutorial on Jmol Application series.
00:06 In this tutorial, we will go through:
00:09 * Important features of Jmol Application.
00:12 * Information regarding download and installation on various operating systems.
00:18 * Uses of Jmol Application.
00:21 We will play clippings of video tutorials available in Jmol Application series at our website.
00:29 To follow this tutorial, you should have knowledge of High School chemistry Or Basic Organic Chemistry.
00:37 To record this tutorial, I am using:* Ubuntu OS version 12.10
00:43 * Jmol version 14.1.11
  • Java version 7

and* Mozilla Firefox Browser 35.0

00:53 About Jmol Application:

Jmol is a molecular viewer for three-dimensional chemical structures and macromolecules.

01:02 Jmol can be used to create and edit 3D models of chemical structures.
01:08 This software can be used by students, educators and researchers in chemistry and biochemistry.
01:16 Here are some important features of Jmol.
01:19 It is a Free and Open Source Software.
01:22 Works on Windows, Mac Operating System, Linux and also on android devices.
01:30 It supports all major web browsers.
01:33 No special hardware is required for high quality 3D-rendering.
01:38 Images can be exported to various file formats such as: jpg, png, gif, pdf etc.
01:47 Reads various file formats such as: pdb, cif, mol, cml, xyz etc.
01:56 If you are connected to internet, you can directly load models on Jmol panel:
02:02 From databases such as pubchem for chemical structures.
02:07 And PDB database for proteins and macromolecules.
02:12 More information about this software is available at the following links.
02:18 Uses of Jmol :

Jmol can be used as a teaching tool to explain concepts in chemistry.

02:26 And for producing high quality 3D images that can be used in print media such as journals, publications and books.
02:36 And also for presentations in classrooms and lectures.
02:41 Jmol can also be used for molecular modelling and producing animation movies.
02:48 Here is the webpage that describes how to incorporate Jmol images in powerpoint presentations.
02:56 Jmol can be effectively used to teach certain topics in chemistry which require 3D visualization.
03:03 At Basic level, topics such as:* Structure and functional groups.
03:08 * Atomic and Molecular orbitals.
03:11 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.
03:22 * Symmetry and point-groups. * Crystal Structure and Unit cell
03:27 And Predict proton NMR spectrum for molecules.
03:31 This feature is available in Jmol version 14.0 and above.
03:36 Jmol can be used to study Structure Activity Relationships.
03:41 Let's see how to download and install Jmol.
03:44 Jmol can be installed on Windows, Mac operating system and on Linux systems.
03:51 A special version of Jmol for Android devices is available at the link shown below.
03:57 For Linux operating systems, download using Ubuntu software center or Synaptic package manager.
04:04 Follow this tutorial in the linux series on our website.
04:08 For Windows and Mac operating systems: Open the given link in any web browser.
04:15 I will open this link and quickly go through the contents given on the web-page.
04:20 This web-page gives a lot of general information about Jmol. Scroll-down the page.
04:27 It gives information about the overview, demonstration pages, features.
04:35 To download Jmol, click on the downloads page. Follow the instructions given on the page to download.
04:44 Information about installing and running Jmol is also given on this page.
04:50 I have created a series of tutorials which describe how to use this software.
04:56 The first tutorial Introduction to Jmol Application has information regarding the various features available on Jmol window.
05:04 Here is the video clipping of that video.
05:07
05:13 To create and edit molecular models, follow the tutorial Create and Edit.

Here is the clipping.

05:18 ---- Add Video Clip------
05:27 We can measure bond lengths, bond angles and dihedral angles. Here is the video clipping.
05:34
05:40 Using Jmol, we can show surfaces and create atomic and molecular orbitals.

Here is the video clipping.

05:47
05:56 This video explains how to show Plane of symmetry and point-groups.

Here is the video clipping.

06:02
06:09 Crystal structures and unit cell can be viewed using Jmol. Here is the video clipping.
06:17
06:24 Here is the video clipping to show proteins and macromolecules in Jmol.
06:29
06:37 A simulated H NMR spectrum can be displayed for all the molecules listed in chemical structure database: Starting from Jmol version 14.0
06:49 Let me open Jmol window and demonstrate this feature.
06:54 To view simulated proton NMR: Go to tools menu.
06:59 Scroll-down to Spectra and click on Spectrum.
07:04 The Jspecview window opens.
07:08 Scroll-down the File menu, click on Add simulation.
07:13 In the dialog-box, enter the name of the molecule.
07:17 Let us type "nitrobenzene", click on OK button.
07:22 A proton NMR spectrum of nitrobenzene is displayed on the panel.
07:28 Atoms on the structure are correlated with signals in the spectrum.
07:33 Certain files include information about molecular vibrations such as GAMESS .log files and Spartan output files.
07:45 We can open these files in Jmol and view vibrations.
07:50 Let me open a log file showing vibrations in carbondioxide molecule.
08:00 Here is an animation, showing vibrations in benzene molecule.
08:05 Here is the animation showing conformations in cyclohexane molecule.
08:15 Let us summarize. In this tutorial, we have learnt:
08:19 * Important features of Jmol Application
08:22 * Information regarding Installation on various operating systems
  • Uses of Jmol Application.
08:29 We have also seen clippings of video tutorials in Jmol Application series.
08:35 And, some animation videos showing vibrations and conformations of cyclohexane.
08:42 The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.
08:48 The Spoken Tutorial project team conducts workshops and gives certificates for those who pass an online test.

For more details, please write to us.

08:59 Spoken Tutorial project is funded by NMEICT, MHRD, Government of India.

More information on this mission is available at the link shown.

09:09 This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14

Retrieved from "https://script.spoken-tutorial.org/index.php?title=Jmol-Application/C2/Overview-of-Jmol-Application/English-timed&oldid=25615"