Difference between revisions of "JChemPaint/C2/Introduction-to-JChemPaint/English-timed"

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(Created page with "{| border=1 || Visual Cue || Narration |- | 00:00 | Hello everyone. Welcome to this tutorial on '''Introduction to JChemPaint'''. |- | 00:06 | In this tutorial, we will lea...")
 
 
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{| border=1
 
{| border=1
−
|| Visual Cue
+
|| Time
 
|| Narration
 
|| Narration
  
Line 13: Line 13:
 
|-
 
|-
 
| 00:08
 
| 00:08
−
| * About '''JChemPaint'''
+
| About '''JChemPaint'''
  
 
|-
 
|-
 
| 00:10
 
| 00:10
−
| * Install '''JChemPaint''' on '''Windows OS'''
+
| Install '''JChemPaint''' on '''Windows Operating system'''
  
 
|-
 
|-
 
| 00:13
 
| 00:13
−
| * Install '''JChemPaint''' on '''Ubuntu OS''' 12.04.  
+
| Install '''JChemPaint''' on '''Ubuntu OS''' 12.04.  
−
 
+
−
|-
+
−
| 00:17
+
−
| We will also learn,
+
  
 
|-
 
|-
 
| 00:18
 
| 00:18
−
| * '''Menu bar, Tool bars''' and '''Panel''' of '''JChemPaint interface''',
+
| We will also learn:
  
 
|-
 
|-
−
| 00:23
+
| 00:20
−
| *'''Preferences''' window
+
| '''Menu bar, Tool bars''' and '''Panel''' of '''JChemPaint interface'''  
  
 
|-
 
|-
 
| 00:25
 
| 00:25
−
| * Draw structures using tools and
+
|'''Preferences''' window
  
 
|-
 
|-
 
| 00:27
 
| 00:27
−
| * Save the drawing with '''.mol''' extension
+
| Draw structures using tools and
  
 
|-
 
|-
−
| 00:31
+
| 00:30
−
| To record this tutorial I am using, '''Ubuntu Linux OS''' version 12.04
+
| Save the drawing with ''''.mol'''' extension.
  
 
|-
 
|-
−
| 00:37
+
| 00:34
−
| *'''Windows''' version 7
+
| To record this tutorial, I am using: * '''Ubuntu Linux OS''' version '''12.04'''
  
 
|-
 
|-
−
| 00:39
+
| 00:41
−
| *'''JChemPaint''' version 3.3-1210
+
| '''Windows''' version '''7'''
  
 
|-
 
|-
−
| 00:44
+
| 00:43
−
| *'''FireFox Browser''' 31.0
+
| '''JChemPaint''' version '''3.3-1210'''
  
 
|-
 
|-
−
| 00:47
+
| 00:48
−
| *'''Java''' version 7
+
| '''FireFox Browser''' '''31.0'''
  
 
|-
 
|-
−
| 00:49
+
| 00:52
−
| To follow this tutorial you must have,
+
| '''Java''' version '''7'''.
  
 
|-
 
|-
−
| 00:51
+
| 00:55
−
| * Internet connection  
+
| To follow this tutorial, you should have:* Internet connection  
  
 
|-
 
|-
−
| 00:53
+
| 00:59
−
| * '''Synaptic Package Manager''' installed on your system.
+
| '''Synaptic Package Manager''' installed on your system
  
 
|-
 
|-
−
| 00:57
+
| 01:03
−
| * Knowledge of '''Terminal on Ubuntu'''.
+
| Knowledge of '''Terminal''' on '''Ubuntu'''  
  
 
|-
 
|-
−
| 01:00
+
| 01:06
−
| * Knowledge of '''Command Prompt on Windows'''.
+
| Knowledge of '''Command Prompt''' on '''Windows'''.
  
 
|-
 
|-
−
| 01:03
+
| 01:10
−
| Please note to run '''JChemPaint''' you should have '''Java''' installed on your system.  
+
| Please note, to run '''JChemPaint''', you should have '''Java''' installed on your system.  
  
 
|-
 
|-
−
| 01:08
+
| 01:16
−
| '''Java''' can be installed on '''Ubuntu''' using '''Synaptic Package Manager'''
+
| '''Java''' can be installed on '''Ubuntu''' using '''Synaptic Package Manager'''.
  
 
|-
 
|-
−
| 01:14
+
| 01:21
 
| For example: '''openjdk-7-jre'''
 
| For example: '''openjdk-7-jre'''
  
 
|-
 
|-
−
| 01:19
+
| 01:27
 
| Let's learn about '''JChemPaint'''.
 
| Let's learn about '''JChemPaint'''.
  
 
|-
 
|-
−
| 01:21
+
| 01:30
−
| * '''JChemPaint''' is a 2D chemical structures editor and viewer.
+
| '''JChemPaint''' is a '''2D chemical structures editor''' and '''viewer'''.
  
 
|-
 
|-
−
| 01:26
+
| 01:35
−
| *It is free and open-source cross platform application developed in '''Java'''.  
+
| It is free and open-source cross platform application developed in '''Java'''.  
  
 
|-
 
|-
−
| 01:32
+
| 01:43
−
| *It allows to import and export structure data in plain-text formats like '''SMILES, Molfile, CML''' and '''InChi keys'''.  
+
|It allows to '''import''' and '''export''' '''structure data''' in plain-text formats like- '''SMILES, Molfile, CML''' and '''InChi keys'''.  
  
 
|-
 
|-
−
| 01:44
+
| 01:56
 
| Let's  start with '''JChemPaint''' installation on '''Ubuntu''' 12.04 OS.
 
| Let's  start with '''JChemPaint''' installation on '''Ubuntu''' 12.04 OS.
  
 
|-
 
|-
−
| 01:51
+
| 02:02
−
| Open '''Firefox''' web browser.  
+
| Open '''Firefox''' web-browser.  
  
 
|-
 
|-
−
| 01:53
+
| 02:06
−
| In the address bar, type the URL  http://jchempaint.github.io/  to install '''JChemPaint''' on '''Ubuntu'''.  
+
| In the address bar, type the URL: http://jchempaint.github.io/  to install '''JChemPaint''' on '''Ubuntu'''.  
  
 
|-
 
|-
−
| 02:05
+
| 02:21
−
| You will be directed to the download page of '''JChemPaint'''.
+
| You will be directed to the '''download page''' of '''JChemPaint'''.
  
 
|-
 
|-
−
| 02:09
+
| 02:26
 
| On the webpage, locate '''“download a recent jar file from github (current is 3.3-1210):”'''
 
| On the webpage, locate '''“download a recent jar file from github (current is 3.3-1210):”'''
  
 
|-
 
|-
−
| 02:19
+
| 02:37
−
| Click on '" the desktop application (6.8 MB).'''
+
| Click on '''"the desktop application (6.8 MB)".'''
  
 
|-
 
|-
−
| 02:25
+
| 02:42
−
| Save file dialog box opens, click on '''Save File''' button.
+
| Save file dialog-box opens. Click on '''Save File''' and click on '''OK'''.
  
 
|-
 
|-
−
| 02:31
+
| 02:48
 
| Let's move the saved file from '''Downloads''' folder to '''Desktop'''.
 
| Let's move the saved file from '''Downloads''' folder to '''Desktop'''.
  
 
|-
 
|-
−
| 02:35
+
| 02:53
−
| Right click on the saved file and select '''Move to Desktop'''.
+
| Right-click on the saved file and select '''Move to Desktop'''.
  
 
|-
 
|-
−
| 02:42
+
| 03:00
 
| To open a new '''JChemPaint''' window, we need '''Terminal.'''  
 
| To open a new '''JChemPaint''' window, we need '''Terminal.'''  
  
 
|-
 
|-
−
| 02:46
+
| 03:04
−
| Press '''CTRl+ALt''' and '''T''' keys simultaneously  to open the '''Terminal'''.
+
| Press '''CTRl+Alt''' and '''T''' keys simultaneously  to open the '''Terminal'''.
  
 
|-
 
|-
−
| 02:52
+
| 03:10
−
| Type '''“cd space Desktop”''' and press '''Enter'''.
+
| Type: '''“cd space Desktop”''' and press '''Enter'''.
  
 
|-
 
|-
−
| 02:58
+
| 03:16
−
| Type '''java space  -jar space ./jchempaint-3.3-1210.jar''' and press '''Enter'''.
+
| Type: '''java space  -jar space ./jchempaint-3.3-1210.jar''' and press '''Enter'''.
  
 
|-
 
|-
−
|  03:14
+
|  03:32
 
| '''JChemPaint''' window opens.
 
| '''JChemPaint''' window opens.
  
 
|-
 
|-
−
|  03:17
+
|  03:35
−
| Please note '''JChemPaint''' can be opened  through the '''Terminal''' only.   
+
| Please note, '''JChemPaint''' can be opened  through the '''Terminal''' only.   
  
 
|-
 
|-
−
| 03:22
+
| 03:41
 
| Let's move on to '''Windows''' installation process.
 
| Let's move on to '''Windows''' installation process.
  
 
|-
 
|-
−
| 03:26
+
| 03:45
 
| Let's  install '''Java''' on '''Windows OS'''.
 
| Let's  install '''Java''' on '''Windows OS'''.
  
 
|-
 
|-
−
| 03:29
+
| 03:50
 
| Open '''Firefox''' web browser on your '''Windows''' machine.
 
| Open '''Firefox''' web browser on your '''Windows''' machine.
  
 
|-
 
|-
−
| 03:33
+
| 03:55
−
| In the address bar, type  '''jre-7-downloads''' and press '''Enter'''.
+
| In the address bar, type: '''jre-7-downloads''' and press '''Enter'''.
  
 
|-
 
|-
−
| 03:41
+
| 04:02
 
| A new webpage opens.
 
| A new webpage opens.
  
 
|-
 
|-
−
| 03:44
+
| 04:06
−
| Click on the link '''Java SE Runtime Environment 7 Downloads-Oracle.'''  
+
| Click on the link '''"Java SE Runtime Environment 7 Downloads-Oracle".'''  
  
 
|-
 
|-
−
| 03:52
+
| 04:14
 
| Download page opens.
 
| Download page opens.
  
 
|-
 
|-
−
| 03:56
+
| 04:17
 
| On the web page, accept the '''License agreement'''.
 
| On the web page, accept the '''License agreement'''.
  
 
|-
 
|-
−
| 03:59
+
| 04:22
−
| Select '''jre-7-windows-i586.exe''' link.
+
| Select '''jre-7-windows-i586.exe''' link.
  
 
|-
 
|-
−
| 04:07
+
| 04:31
−
|  '''Save file''' dialog box opens.  
+
|  '''Save File''' dialog-box opens.  
  
 
|-
 
|-
−
| 04:10
+
| 04:35
 
| Click on '''Save File''' button.
 
| Click on '''Save File''' button.
  
 
|-
 
|-
−
| 04:12
+
| 04:38
−
| The file will be downloaded in the '''Downloads''' folder.
+
| The file will be downloaded into the '''Downloads''' folder.
  
 
|-
 
|-
−
| 04:16
+
| 04:42
−
| “Click on the downloaded file.  
+
| Click on the downloaded file.  
  
 
|-
 
|-
−
| 04:19
+
| 04:46
 
| Follow the installation process to install '''Java'''.
 
| Follow the installation process to install '''Java'''.
  
 
|-
 
|-
−
| 04:27
+
| 04:51
 
| Click on '''Close'''.
 
| Click on '''Close'''.
  
 
|-
 
|-
−
| 04:29
+
| 04:54
−
| '''Jre-7''' will be installed on your machine.
+
| '''Jre-7''' will be installed on your system.
  
 
|-
 
|-
−
| 04:33
+
| 04:59
 
| Let's install '''JChemPaint'''.
 
| Let's install '''JChemPaint'''.
  
 
|-
 
|-
−
| 04:35
+
| 05:02
 
| Open '''Firefox''' web browser on your '''Windows''' machine.
 
| Open '''Firefox''' web browser on your '''Windows''' machine.
  
 
|-
 
|-
−
| 04:39
+
| 05:06
−
| In the address bar, type the '''URL http://jchempaint.github.io/ ''' to install '''JChemPaint''' on '''Windows'''.
+
| In the address bar, type the URL: http://jchempaint.github.io/ to install '''JChemPaint''' on '''Windows'''.
  
 
|-
 
|-
−
| 04:50
+
| 05:21
 
| You will be directed to the download page of  '''JChemPaint'''.
 
| You will be directed to the download page of  '''JChemPaint'''.
  
 
|-
 
|-
−
| 04:55
+
| 05:26
−
| On the webpage, locate
+
| On the webpage, locate '''“download a recent jar file from github (current is 3.3-1210):”'''
  
 
|-
 
|-
−
| 04:57
+
| 05:39
−
| '''“download a recent jar file from github (current is 3.3-1210):”'''
+
| Click on  '''"the desktop application (6.8 MB)"'''.
  
 
|-
 
|-
−
| 05:04
+
| 05:44
−
| Click on  '''"the desktop application (6.8 MB) "'''.
+
| '''Save file''' dialog-box opens.  
  
 
|-
 
|-
−
| 05:09
+
| 05:47
−
| '''Save file''' dialog box opens.
+
−
 
+
−
|-
+
−
| 05:12
+
 
| Click on '''Save File''' button.
 
| Click on '''Save File''' button.
  
 
|-
 
|-
−
| 05:15
+
| 05:51
−
| The '''.jar''' file will be downloaded to '''Downloads''' folder.
+
| The ''''.jar'''' file will be downloaded to '''Downloads''' folder.
  
 
|-
 
|-
−
| 05:19
+
| 05:57
−
| Open '''Downloads''' folder and select the file '''jchempaint-3.3-1210.jar.'''  
+
| Open '''Downloads''' folder and select the file ''''jchempaint-3.3-1210.jar'.'''  
  
 
|-
 
|-
−
| 05:28
+
| 06:08
 
| You can download available latest version.
 
| You can download available latest version.
  
 
|-
 
|-
−
| 05:32
+
| 06:13
−
| Right click on the executable file.  
+
| Right-click on the executable file.  
  
 
|-
 
|-
−
| 05:35
+
| 06:16
 
| Select '''Open''' to open '''JChemPaint'''.
 
| Select '''Open''' to open '''JChemPaint'''.
  
 
|-
 
|-
−
| 05:38
+
| 06:20
 
| Alternately, you can open '''JChemPaint''' using '''Command prompt.'''
 
| Alternately, you can open '''JChemPaint''' using '''Command prompt.'''
  
 
|-
 
|-
−
| 05:43
+
| 06:26
 
| To open '''Command prompt''', press '''Windows''' and '''R''' keys simultaneously on the keyboard.  
 
| To open '''Command prompt''', press '''Windows''' and '''R''' keys simultaneously on the keyboard.  
  
 
|-
 
|-
−
| 05:50
+
| 06:34
 
| '''Run prompt''' box opens.
 
| '''Run prompt''' box opens.
  
 
|-
 
|-
−
| 05:53
+
| 06:37
−
| In the '''Open box''' type '''“cmd”''' and click on '''OK'''.
+
| In the '''Open box''', type: '''“cmd”''' and click on '''OK'''.
  
 
|-
 
|-
−
| 05:58
+
| 06:43
 
| '''Command prompt''' opens.
 
| '''Command prompt''' opens.
  
 
|-
 
|-
−
| 06:00
+
| 06:46
−
| Let's go to '''Downloads''' folder where we have downloaded our '''.jar''' file.  
+
| Let's go to '''Downloads''' folder where we have saved our downloaded  ''''.jar'''' file.  
  
 
|-
 
|-
−
| 06:07
+
| 06:54
−
| Type at the '''prompt “cd space Downloads”''' and press '''Enter'''.   
+
| Type at the prompt: '''cd space Downloads''' and press '''Enter'''.   
  
 
|-
 
|-
−
| 06:14
+
| 07:00
−
| Type '''java space -jar space jchempaint-3.3-1210.jar''' and press '''Enter'''.
+
| Type: '''java space -jar space jchempaint-3.3-1210.jar''' and press '''Enter'''.
  
 
|-
 
|-
−
| 06:27
+
| 07:13
 
| '''JChemPaint''' window opens.
 
| '''JChemPaint''' window opens.
  
 
|-
 
|-
−
| 06:30
+
| 07:17
 
|  If an error appears on '''command prompt''',  
 
|  If an error appears on '''command prompt''',  
  
 
|-
 
|-
−
| 06:34
+
| 07:20
−
| *Go to '''Program files''' locate the '''java''' folder and click on it.
+
| Go to '''Program files''', locate the '''java''' folder and click on it.
  
 
|-
 
|-
−
| 06:39
+
| 07:27
−
| *Locate '''bin''' folder and right-click on it.
+
| Locate '''bin''' folder and right-click on it.
  
 
|-
 
|-
−
| 06:43
+
| 07:32
−
| *Navigate to '''Properties'''.
+
| Navigate to '''Properties'''.
  
 
|-
 
|-
−
| 06:44
+
| 07:35
−
| *Copy the address '''C:\Program Files''' within brackets '''(x86)\Java\jre7.'''
+
| Copy the address '''C:\Program Files''' within brackets '''(x86)\Java\jre7.'''
  
 
|-
 
|-
−
| 06:55
+
| 07:48
−
| To set the path follow the steps.
+
| To set the path, follow the steps.
  
 
|-
 
|-
−
| 06:58
+
| 07:51
−
| *Right-click on '''My Computer''', select '''Properties''' option.  
+
| Right-click on '''My Computer''', select '''Properties''' option.  
  
 
|-
 
|-
−
| 07:02
+
| 07:57
−
| *Click on '''Advanced System settings''', and then click on '''Environment  Variables.'''  
+
| Click on '''Advanced System settings''' and then click on '''Environment  Variables.'''  
  
 
|-
 
|-
−
| 07:08
+
| 08:04
−
| *In '''System Variables''' search for '''Path'''.
+
| In '''System Variables''', search for '''Path'''.
  
 
|-
 
|-
−
| 07:12
+
| 08:09
−
| *Click on '''Edit'''.
+
| Click on '''Edit'''.
  
 
|-
 
|-
−
| 07:13
+
| 08:11
−
| *'''Edit system  Variable''' dialog box opens
+
| '''Edit system  Variable''' dialog-box opens.
  
 
|-
 
|-
−
| 07:17
+
| 08:16
−
| *Paste the address  '''C:\Program Files''' within brackets '''(x86)\Java\jre7.'''
+
| '''Paste''' the address  '''C:\Program Files''' within brackets '''(x86)\Java\jre7.'''
  
 
|-
 
|-
−
| 07:27
+
| 08:28
−
| *Click on '''OK ''' and close the windows.
+
| Click on '''OK ''' and close the windows.
  
 
|-
 
|-
−
| 07:30
+
| 08:32
 
| '''JChemPaint''' window looks like this.
 
| '''JChemPaint''' window looks like this.
  
 
|-
 
|-
−
| 07:33
+
| 08:36
−
| This the '''Menu bar'''.
+
| This is the '''Menu bar'''.
  
 
|-
 
|-
−
| 07:34
+
| 08:38
−
| '''Menu bar''' contains menu items like:
+
| '''Menu bar''' contains menu items like: '''File, Edit, View, Atom, Bond, Tools, R-groups, Templates''' and '''Help'''.
−
 
+
−
'''File, Edit, View, Atom, Bond, Tools, R-groups, Templates''' and '''Help'''.
+
  
 
|-
 
|-
−
| 07:49
+
| 08:54
−
| '''Tool bars''' contain all the tools required for  you to work with '''JChemPaint'''.  
+
| '''Tool bar''' contains all the tools required for  you to work with JChemPaint.  
  
 
|-
 
|-
−
| 07:55
+
| 09:02
−
| '''JChempaint''' window has,
+
| '''JChempaint''' window has-
  
 
|-
 
|-
−
| 07:56
+
| 09:04
−
| *Formatting tools on top
+
| Formatting tools on the top
  
 
|-
 
|-
−
| 08:00
+
| 09:07
−
| *Bond tools on the left
+
| '''Bond''' tools on the left
  
 
|-
 
|-
−
| 08:03
+
| 09:09
−
| *Ring tools on the right and
+
| '''Ring''' tools on the right and
 
   
 
   
 
|-
 
|-
−
| 08:06
+
| 09:12
−
| *Element tools at the bottom
+
| Element tools at the bottom
  
 
|-
 
|-
−
| 08:10
+
| 09:15
 
| '''Panel''' displays the drawn structures.
 
| '''Panel''' displays the drawn structures.
  
 
|-
 
|-
−
| 08:13
+
| 09:18
−
| Now to '''JChemPaint  Preferences''' window.
+
| Now, to '''JChemPaint  Preferences''' window.
  
 
|-
 
|-
−
| 08:16
+
| 09:22
 
| Click on '''Draw a chain''' tool.
 
| Click on '''Draw a chain''' tool.
  
 
|-
 
|-
−
| 08:18
+
| 09:24
−
| Click and drag the '''chain'''  to '''6 Carbon atoms''' on the '''Panel'''.
+
| Click and drag the '''chain'''  to 6 Carbon atoms on the '''Panel'''.
  
 
|-
 
|-
−
| 08:24
+
| 09:30
−
| Notice that '''Carbon chain''' does not contain any '''atoms'''.
+
| Notice that '''Carbon chain''' does not contain any atoms.
  
 
|-
 
|-
−
| 08:29
+
| 09:35
 
| Go to '''Edit''' menu, navigate to '''Preferences''' and click on it.
 
| Go to '''Edit''' menu, navigate to '''Preferences''' and click on it.
  
 
|-
 
|-
−
| 08:35
+
| 09:42
 
| '''Preferences''' window opens.
 
| '''Preferences''' window opens.
  
 
|-
 
|-
−
| 08:38
+
| 09:45
−
| '''Preferences''' window has two tabs '''Display Preferences''' and '''Other Preferences'''.
+
| '''Preferences''' window has two tabs- '''Display Preferences''' and '''Other Preferences'''.
  
 
|-
 
|-
−
| 08:44
+
| 09:54
−
| By default '''Display Preferences''' tab is selected.
+
| By default, '''Display Preferences''' tab is selected.
  
 
|-
 
|-
−
| 08:48
+
| 10:00
−
| Notice that none of  the check boxes are selected here.
+
| Notice that none of  the check-boxes are selected.
  
 
|-
 
|-
−
| 08:52
+
| 10:05
−
| Let's click on a few check boxes and see how they are useful.
+
| Let's click on a few check-boxes and see how they are useful.
−
 
+
  
 
|-
 
|-
−
| 08:57
+
|10:12
−
| To show '''Methyl groups''' on the '''chain''' click on '''Show explicit methyl groups.'''
+
| To show '''Methyl groups''' on the '''chain''', click on '''Show explicit methyl groups.'''
  
 
|-
 
|-
−
| 09:03
+
| 10:18
−
| To show '''hydrogens''' click on '''Show implicit hydrogens.'''
+
| To show '''hydrogens''', click on '''Show implicit hydrogens.'''
  
 
|-
 
|-
−
| 09:08
+
| 10:23
 
| Click on '''Apply''' and '''OK''' buttons to apply the changes.
 
| Click on '''Apply''' and '''OK''' buttons to apply the changes.
  
 
|-
 
|-
−
| 09:12
+
| 10:29
−
| As an example let's draw '''Phosphoric acid(H3PO4)'''.
+
| As an example, let's draw '''Phosphoric acid(H3PO4)'''.
  
 
|-
 
|-
−
| 09:18
+
| 10:35
 
| To draw, click on '''Phosphrous(P) tool''' and then click on the '''Panel'''.
 
| To draw, click on '''Phosphrous(P) tool''' and then click on the '''Panel'''.
  
 
|-
 
|-
−
| 09:23
+
| 10:42
−
| '''Phosphine(PH3)''' will be displayed
+
| '''Phosphine(PH3)''' will be displayed.
  
 
|-
 
|-
−
| 09:26
+
| 10:46
−
| Click on '''Oxygen(O) tool''' and click on '''Single bond tool.'''
+
| Click on '''Oxygen(O) tool''' and then click on '''Single bond tool.'''
  
 
|-
 
|-
−
| 09:31
+
| 10:51
−
| Place the cursor on '''P''';  a small 'blue' colored circle appears on it.
+
| Place the cursor on 'P';  a small 'blue' colored circle appears on it.
  
 
|-
 
|-
−
| 09:37
+
| 10:57
−
| Click on '''P''' and drag to draw four '''Hydroxy bonds'''.
+
| Click on 'P' and drag to draw four '''Hydroxy bonds'''.
  
 
|-
 
|-
−
| 09:43
+
| 11:02
−
| You will notice a red line below '''Phosphrous atom'''.
+
| You will notice a red line, below '''Phosphrous''' atom.
  
 
|-
 
|-
−
| 09:47
+
| 11:07
 
| This indicates that '''valency''' is not complete.
 
| This indicates that '''valency''' is not complete.
  
 
|-
 
|-
−
| 09:51
+
| 11:11
−
| To complete the '''valency''' let's make the top '''Phosphrous-hydroxy bond''' as a '''double bond'''.  
+
| To complete the '''valency''', let's make the top '''Phosphrous-hydroxy bond''' as a '''double bond'''.  
  
 
|-
 
|-
−
| 09:57
+
| 11:19
 
| Click on '''double bond tool'''.
 
| Click on '''double bond tool'''.
  
 
|-
 
|-
−
| 10:00
+
| 11:21
 
| Click on top '''Phosphrous-hydroxy bond'''.
 
| Click on top '''Phosphrous-hydroxy bond'''.
  
 
|-
 
|-
−
| 10:05
+
| 11:26
 
| The obtained structure is '''Phosphoric acid'''.   
 
| The obtained structure is '''Phosphoric acid'''.   
  
 
|-
 
|-
−
| 10:09
+
| 11:30
 
|  Notice that all the atoms in the structure are black colored.
 
|  Notice that all the atoms in the structure are black colored.
  
 
|-
 
|-
−
| 10:14
+
| 11:36
−
| To show '''Rasmol''' color of the element,
+
| To show '''Rasmol''' color of the element-
  
 
|-
 
|-
−
| 10:17
+
| 11:39
 
| Go to '''Edit''' menu and navigate to '''Preferences'''.
 
| Go to '''Edit''' menu and navigate to '''Preferences'''.
  
 
|-
 
|-
−
| 10:21
+
| 11:44
−
|  In the window click on '''Color atoms by element''' check box.
+
|  In the window, click on '''Color atoms by element''' check-box.
  
 
|-
 
|-
−
| 10:26
+
| 11:50
 
| It shows '''Rasmol''' color of the element.
 
| It shows '''Rasmol''' color of the element.
  
 
|-
 
|-
−
| 10:29
+
| 11:55
 
|  Click on '''Apply''' and '''OK''' buttons to apply the changes.
 
|  Click on '''Apply''' and '''OK''' buttons to apply the changes.
  
 
|-
 
|-
−
| 10:34
+
| 12:00
 
| Note that elements appear with their  '''Rasmol''' colors.
 
| Note that elements appear with their  '''Rasmol''' colors.
  
 
|-
 
|-
−
| 10:39
+
| 12:05
 
| Let's save the file.
 
| Let's save the file.
  
 
|-
 
|-
−
| 10:41
+
| 12:07
−
| Click on '''File menu''' and select '''Save as....'''  
+
| Click on '''File''' menu and select '''Save as.'''  
  
 
|-
 
|-
−
| 10:45
+
| 12:12
−
| '''Save as''' dialog box opens.
+
| '''Save as''' dialog-box opens.
  
 
|-
 
|-
−
| 10:48
+
| 12:15
 
| Select '''Desktop''' folder to save the file on '''Desktop'''.
 
| Select '''Desktop''' folder to save the file on '''Desktop'''.
  
 
|-
 
|-
−
| 10:52
+
| 12:21
−
|  Type the file name as '''Phosphoric acid''' and  click on '''Save''' button.
+
|  Type the file name as "Phosphoric acid" and  click on '''Save''' button.
  
 
|-
 
|-
−
| 10:56
+
| 12:27
−
| The file will be saved with '''.mol''' extension.
+
| The file will be saved with ''''.mol'''' extension.
  
 
|-
 
|-
−
| 11:01
+
| 12:31
−
| Let's summarise,
+
| Let's summarize.
  
 
|-
 
|-
−
| 11:03
+
| 12:33
−
| In this tutorial, we have learnt  
+
| In this tutorial, we have learnt:
  
 
|-
 
|-
−
| 11:05
+
| 12:36
−
| * About '''JChemPaint'''
+
| About '''JChemPaint'''
  
 
|-
 
|-
−
| 11:07
+
| 12:38
−
| * Install  '''JChemPaint''' on''' Windows OS'''
+
| Install  '''JChemPaint''' on''' Windows Operating System'''
  
 
|-
 
|-
−
| 11:10
+
| 12:42
−
| * Install  '''JChemPaint''' on '''Ubuntu OS''' 12.04  
+
| Install  '''JChemPaint''' on '''Ubuntu Operating system''' 12.04  
  
 
|-
 
|-
−
| 11:14
+
| 12:47
−
| * '''Menu bar, Tool bars''' and '''Panel''' of  '''JChemPaint''' interface  
+
| '''Menu bar, Tool bar''' and '''Panel''' of  '''JChemPaint''' interface  
  
 
|-
 
|-
−
| 11:19
+
| 12:52
−
| * '''Preferences''' window
+
| '''Preferences''' window
  
 
|-
 
|-
−
| 11:20
+
| 12:55
−
| * Draw structures using tools and
+
| Draw structures using tools and
  
 
|-
 
|-
−
| 11:23
+
| 12:58
−
| * Save the drawing with '''.mol''' extension
+
| Save the drawing with ''''.mol'''' extension.
  
 
|-
 
|-
−
| 11:27
+
| 13:02
−
|  As an assignment
+
|  As an assignment-
  
 
|-
 
|-
−
| 11:28
+
| 13:04
−
| * Install '''JChemPaint'''.
+
| Install '''JChemPaint'''.
  
 
|-
 
|-
−
| 11:30
+
| 13:06
−
| * Explore various '''menu''' items.
+
| Explore various '''menu''' items.
  
 
|-
 
|-
−
| 11:33
+
| 13:09
−
| This video summarises the Spoken Tutorial project
+
| This video summarizes the '''Spoken Tutorial''' project.
  
 
|-
 
|-
−
| 11:37
+
| 13:12
 
| 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.
  
 
|-
 
|-
−
| 11:41
+
| 13:18
−
| The Spoken Tutorial  Team: Conducts workshops using spoken tutorials
+
| The Spoken Tutorial  Team: * Conducts workshops using spoken tutorials.
  
 
|-
 
|-
−
| 11:43
+
| 13:22
−
| Gives certificates to those who pass an online test  
+
|Gives certificates to those who pass an online test.
  
 
|-
 
|-
−
| 11:46
+
| 13:27
−
| For more details, please write to  
+
| For more details, please write to: contact@spoken-tutorial.org  
−
contact@spoken-tutorial.org  
+
  
 
|-
 
|-
−
| 11:53
+
| 13:34
−
| Spoken Tutorial Project is a part of the Talk to a Teacher project  
+
| '''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project.
  
 
|-
 
|-
−
| 11:57
+
| 13:39
−
| 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.
  
 
|-
 
|-
−
| 12:04
+
| 13:46
−
| More information on this Mission is available at http://spoken-tutorial.org/NMEICT-Intro ]
+
| More information on this mission is available at this link: http://spoken-tutorial.org/NMEICT-Intro
  
 
|-
 
|-
−
| 12:09
+
| 13:52
−
| This is Madhuri Ganpathi from IIT Bombay signing off. Thank you for joining.  
+
| This is Madhuri Ganpathi from '''IIT Bombay''', signing off. Thank you for joining.  
  
 
|-
 
|-
 
|}
 
|}

Latest revision as of 16:21, 28 March 2017

Time Narration
00:00 Hello everyone. Welcome to this tutorial on Introduction to JChemPaint.
00:06 In this tutorial, we will learn:
00:08 About JChemPaint
00:10 Install JChemPaint on Windows Operating system
00:13 Install JChemPaint on Ubuntu OS 12.04.
00:18 We will also learn:
00:20 Menu bar, Tool bars and Panel of JChemPaint interface
00:25 Preferences window
00:27 Draw structures using tools and
00:30 Save the drawing with '.mol' extension.
00:34 To record this tutorial, I am using: * Ubuntu Linux OS version 12.04
00:41 Windows version 7
00:43 JChemPaint version 3.3-1210
00:48 FireFox Browser 31.0
00:52 Java version 7.
00:55 To follow this tutorial, you should have:* Internet connection
00:59 Synaptic Package Manager installed on your system
01:03 Knowledge of Terminal on Ubuntu
01:06 Knowledge of Command Prompt on Windows.
01:10 Please note, to run JChemPaint, you should have Java installed on your system.
01:16 Java can be installed on Ubuntu using Synaptic Package Manager.
01:21 For example: openjdk-7-jre
01:27 Let's learn about JChemPaint.
01:30 JChemPaint is a 2D chemical structures editor and viewer.
01:35 It is free and open-source cross platform application developed in Java.
01:43 It allows to import and export structure data in plain-text formats like- SMILES, Molfile, CML and InChi keys.
01:56 Let's start with JChemPaint installation on Ubuntu 12.04 OS.
02:02 Open Firefox web-browser.
02:06 In the address bar, type the URL: http://jchempaint.github.io/ to install JChemPaint on Ubuntu.
02:21 You will be directed to the download page of JChemPaint.
02:26 On the webpage, locate “download a recent jar file from github (current is 3.3-1210):”
02:37 Click on "the desktop application (6.8 MB)".
02:42 Save file dialog-box opens. Click on Save File and click on OK.
02:48 Let's move the saved file from Downloads folder to Desktop.
02:53 Right-click on the saved file and select Move to Desktop.
03:00 To open a new JChemPaint window, we need Terminal.
03:04 Press CTRl+Alt and T keys simultaneously to open the Terminal.
03:10 Type: “cd space Desktop” and press Enter.
03:16 Type: java space -jar space ./jchempaint-3.3-1210.jar and press Enter.
03:32 JChemPaint window opens.
03:35 Please note, JChemPaint can be opened through the Terminal only.
03:41 Let's move on to Windows installation process.
03:45 Let's install Java on Windows OS.
03:50 Open Firefox web browser on your Windows machine.
03:55 In the address bar, type: jre-7-downloads and press Enter.
04:02 A new webpage opens.
04:06 Click on the link "Java SE Runtime Environment 7 Downloads-Oracle".
04:14 Download page opens.
04:17 On the web page, accept the License agreement.
04:22 Select jre-7-windows-i586.exe link.
04:31 Save File dialog-box opens.
04:35 Click on Save File button.
04:38 The file will be downloaded into the Downloads folder.
04:42 Click on the downloaded file.
04:46 Follow the installation process to install Java.
04:51 Click on Close.
04:54 Jre-7 will be installed on your system.
04:59 Let's install JChemPaint.
05:02 Open Firefox web browser on your Windows machine.
05:06 In the address bar, type the URL: http://jchempaint.github.io/ to install JChemPaint on Windows.
05:21 You will be directed to the download page of JChemPaint.
05:26 On the webpage, locate “download a recent jar file from github (current is 3.3-1210):”
05:39 Click on "the desktop application (6.8 MB)".
05:44 Save file dialog-box opens.
05:47 Click on Save File button.
05:51 The '.jar' file will be downloaded to Downloads folder.
05:57 Open Downloads folder and select the file 'jchempaint-3.3-1210.jar'.
06:08 You can download available latest version.
06:13 Right-click on the executable file.
06:16 Select Open to open JChemPaint.
06:20 Alternately, you can open JChemPaint using Command prompt.
06:26 To open Command prompt, press Windows and R keys simultaneously on the keyboard.
06:34 Run prompt box opens.
06:37 In the Open box, type: “cmd” and click on OK.
06:43 Command prompt opens.
06:46 Let's go to Downloads folder where we have saved our downloaded '.jar' file.
06:54 Type at the prompt: cd space Downloads and press Enter.
07:00 Type: java space -jar space jchempaint-3.3-1210.jar and press Enter.
07:13 JChemPaint window opens.
07:17 If an error appears on command prompt,
07:20 Go to Program files, locate the java folder and click on it.
07:27 Locate bin folder and right-click on it.
07:32 Navigate to Properties.
07:35 Copy the address C:\Program Files within brackets (x86)\Java\jre7.
07:48 To set the path, follow the steps.
07:51 Right-click on My Computer, select Properties option.
07:57 Click on Advanced System settings and then click on Environment Variables.
08:04 In System Variables, search for Path.
08:09 Click on Edit.
08:11 Edit system Variable dialog-box opens.
08:16 Paste the address C:\Program Files within brackets (x86)\Java\jre7.
08:28 Click on OK and close the windows.
08:32 JChemPaint window looks like this.
08:36 This is the Menu bar.
08:38 Menu bar contains menu items like: File, Edit, View, Atom, Bond, Tools, R-groups, Templates and Help.
08:54 Tool bar contains all the tools required for you to work with JChemPaint.
09:02 JChempaint window has-
09:04 Formatting tools on the top
09:07 Bond tools on the left
09:09 Ring tools on the right and
09:12 Element tools at the bottom
09:15 Panel displays the drawn structures.
09:18 Now, to JChemPaint Preferences window.
09:22 Click on Draw a chain tool.
09:24 Click and drag the chain to 6 Carbon atoms on the Panel.
09:30 Notice that Carbon chain does not contain any atoms.
09:35 Go to Edit menu, navigate to Preferences and click on it.
09:42 Preferences window opens.
09:45 Preferences window has two tabs- Display Preferences and Other Preferences.
09:54 By default, Display Preferences tab is selected.
10:00 Notice that none of the check-boxes are selected.
10:05 Let's click on a few check-boxes and see how they are useful.
10:12 To show Methyl groups on the chain, click on Show explicit methyl groups.
10:18 To show hydrogens, click on Show implicit hydrogens.
10:23 Click on Apply and OK buttons to apply the changes.
10:29 As an example, let's draw Phosphoric acid(H3PO4).
10:35 To draw, click on Phosphrous(P) tool and then click on the Panel.
10:42 Phosphine(PH3) will be displayed.
10:46 Click on Oxygen(O) tool and then click on Single bond tool.
10:51 Place the cursor on 'P'; a small 'blue' colored circle appears on it.
10:57 Click on 'P' and drag to draw four Hydroxy bonds.
11:02 You will notice a red line, below Phosphrous atom.
11:07 This indicates that valency is not complete.
11:11 To complete the valency, let's make the top Phosphrous-hydroxy bond as a double bond.
11:19 Click on double bond tool.
11:21 Click on top Phosphrous-hydroxy bond.
11:26 The obtained structure is Phosphoric acid.
11:30 Notice that all the atoms in the structure are black colored.
11:36 To show Rasmol color of the element-
11:39 Go to Edit menu and navigate to Preferences.
11:44 In the window, click on Color atoms by element check-box.
11:50 It shows Rasmol color of the element.
11:55 Click on Apply and OK buttons to apply the changes.
12:00 Note that elements appear with their Rasmol colors.
12:05 Let's save the file.
12:07 Click on File menu and select Save as.
12:12 Save as dialog-box opens.
12:15 Select Desktop folder to save the file on Desktop.
12:21 Type the file name as "Phosphoric acid" and click on Save button.
12:27 The file will be saved with '.mol' extension.
12:31 Let's summarize.
12:33 In this tutorial, we have learnt:
12:36 About JChemPaint
12:38 Install JChemPaint on Windows Operating System
12:42 Install JChemPaint on Ubuntu Operating system 12.04
12:47 Menu bar, Tool bar and Panel of JChemPaint interface
12:52 Preferences window
12:55 Draw structures using tools and
12:58 Save the drawing with '.mol' extension.
13:02 As an assignment-
13:04 Install JChemPaint.
13:06 Explore various menu items.
13:09 This video summarizes the Spoken Tutorial project.
13:12 If you do not have good bandwidth, you can download and watch it.
13:18 The Spoken Tutorial Team: * Conducts workshops using spoken tutorials.
13:22 Gives certificates to those who pass an online test.
13:27 For more details, please write to: contact@spoken-tutorial.org
13:34 Spoken Tutorial project is a part of the Talk to a Teacher project.
13:39 It is supported by the National Mission on Education through ICT, MHRD, Government of India.
13:46 More information on this mission is available at this link: http://spoken-tutorial.org/NMEICT-Intro
13:52 This is Madhuri Ganpathi from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Ranjana, Sandhya.np14

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