JChemPaint/C3/Features-of-JChemPaint/English-timed - Revision history

PoojaMoolya at 10:58, 28 March 2017

2017-03-28T10:58:47Z

PoojaMoolya at 10:57, 28 March 2017

2017-03-28T10:57:20Z

Sandhya.np14 at 12:59, 14 December 2015

2015-12-14T12:59:35Z

Sandhya.np14 at 11:25, 6 December 2015

2015-12-06T11:25:57Z

Sandhya.np14 at 11:07, 6 December 2015

2015-12-06T11:07:41Z

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PoojaMoolya at 06:03, 4 March 2015

2015-03-04T06:03:23Z

Ranjana: Created page with "{| border=1 || '''Visual Cue''' || '''Narration''' |- | 00:01 |Hello everyone. Welcome to this tutorial on '''Features of JChemPaint.'''. |- | 00:07 | In this tutorial, we..."

2015-02-17T10:31:07Z

Created page with "{| border=1 || '''Visual Cue''' || '''Narration''' |- | 00:01 |Hello everyone. Welcome to this tutorial on '''Features of JChemPaint.'''. |- | 00:07 | In this tutorial, we..."

New page

{| border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
| 00:01
|Hello everyone. Welcome to this tutorial on '''Features of JChemPaint.'''.

|-
| 00:07
| In this tutorial, we will learn to change:

|-
| 00:10
| * Background color of the '''Panel'''

|-
| 00:12
| * Look and feel of the window

|-
| 00:14
| * User interface language.

|-
| 00:18
| We will also learn to,

|-
| 00:20
| * Insert '''Templates'''

|-
| 00:22
| * Generate '''SMILES''' and '''InChi''' keys for a given structure.

|-
| 00:26
| * Insert '''SMILES''' and '''InChi''' keys to generate structures.

|-
| 00:31
| To record this tutorial I am using,

|-
| 00:33
| *'''Ubuntu Linux''' OS version 12.04

|-
| 00:38
| *'''JChemPaint''' version 3.3-1210

|-
| 00:43
| *'''Java''' version 7

|-
| 00:46
| To follow this tutorial you should be familiar with '''JChemPaint''' chemical structures editor.

|-
| 00:54
| If not, for relevant tutorial, please visit our website.

|-
| 01:01
| Let's switch to '''JChemPaint''' window.

|-
| 01:04
| Recall that we had saved our '''.jar''' file on the '''Desktop'''.

|-
| 01:10
| Press '''CTRl+ALt''' and '''T''' keys simultaneously to open the '''Terminal'''.

|-
| 01:17
| Type ''''“cd space Desktop”''' and press '''Enter'''.

|-
| 01:24
| Type ''' “java space -jar space ./jchempaint-3.3-1210.jar”''' and press '''Enter'''.

|-
| 01:43
| '''JChemPaint''' window opens.

|-
| 01:45
| Let's see how to change the background color of the '''Panel'''.

|-
| 01:50
| Go to '''Edit''' menu, navigate to '''Preferences''' and click on it.

|-
| 01:56
| '''JChemPaint Preferences''' window opens.

|-
| 02:00
| Click on '''Choose background color''' button.

|-
| 02:04
| '''Choose background color''' window opens.

|-
| 02:07
| This window has three tabs namely '''Swatches, HSB''' and '''RGB'''.

|-
| 02:15
| Depending on your '''Operating System''' this window, may vary a little.

|-
| 02:21
| '''HSB''' may be '''HSV'''.

|-
| 02:25
| You may not see '''Swatches''' tab.

|-
| 02:28
| '''Windows Operating System''' has two additional tabs namely '''HSL''' and '''CMYK'''.

|-
| 02:37
| You can select the background color of your choice.

|-
| 02:40
| I will click on light green color '''Swatch''' to change background color to light green.

|-
| 02:47
| Click on '''OK''' to close the window.

|-
| 02:50
| Click on '''OK''' to close the '''Preferences''' window.

|-
| 02:55
| Try various color combinations using '''Choose background color''' window.

|-
| 03:01
| Next about '''Other Preferences''' tab.

|-
| 03:05
| Go to '''Edit''' menu and click on '''Preferences'''

|-
| 03:09
| '''Preferences''' window opens.

|-
| 03:12
| Click on '''Other Preferences''' tab.

|-
| 03:15
| Go to '''Look and feel''' field.

|-
| 03:19
| This field has a drop down list.

|-
| 03:21
| List contains '''Sytem, Metal, Nimbus, Motif, GTK''' and '''Windows'''.

|-
| 03:29
| I will click on '''Nimbus'''.

|-
| 03:32
| Then click on '''OK''' button.

|-
| 03:35
| Observe the change in look and feel of the window.

|-
| 03:40
| Click on Edit menu then click on '''Preferences'''.

|-
| 03:45
| Click on '''other Preferences'''.

|-
| 03:49
| Go to '''User Interface Language''' field.

|-
| 03:53
| This field has a drop down list.

|-
| 03:56
| List contains '''American English''' and other languages.

|-
| 04:02
| By default '''American English''' is selected.

|-
| 04:06
| I will click on '''Spanish'''.

|-
| 04:09
| Click '''OK''' button.

|-
| 04:12
| Observe the change in language on the '''Menu bar''' and on the '''Status bar'''.

|-
| 04:19
| I will undo the changes.

|-
| 04:23
| Now let's insert '''Templates''' onto the '''Panel'''.

|-
| 04:27
| Click on '''Templates''' menu.

|-
| 04:30
| '''Templates''' drop down opens.

|-
| 04:33
| Alternately you can open '''Templates''' menu from side tool bar.

|-
| 04:39
| Here you can see various '''Templates''' tabs.

|-
| 04:43
| Click on '''All Templates''' tab.

|-
| 04:47
| '''Structure Templates''' window opens.

|-
| 04:51
| Window shows list of '''Templates''' along with their structures.

|-
| 04:56
| I will scroll down the window to view various structures.

|-
| 05:01
| I will click on a few '''Template''' tabs to display structures.

|-
| 05:06
| Click on '''Beta Lactums''' tab.

|-
| 05:10
| Click on '''Penicillin''' structure, to display it on the '''Panel'''.

|-
| 05:16
| Press '''Ctrl+ Z''' to undo the changes.

|-
| 05:20
| Click on '''Templates''' tab, click on '''Miscellaneous'''.

|-
| 05:25
| Then click on '''C60 Fullerene''', to display it on the '''Panel'''.

|-
| 05:31
| You can load other '''Templates''' of your choice onto the '''Panel'''.

|-
| 05:36
| Next we will learn about '''SMILES''' and '''InChi keys'''.

|-
| 05:41
| What are '''SMILES''' and '''InChi Keys'''?

|-
| 05:45
| * '''SMILES''' is simplified molecular input line entry system.

|-
| 05:51
| * It describes chemical structures using short '''ASCII''' strings.

|-
| 05:57
| * Molecular Editors import '''SMILES''' strings, to convert structures into 2D drawings.

|-
| 06:06
| * For example, '''CCCCCC''' is a '''Canonical SMILES''' of '''Hexane'''

|-
| 06:15
| * '''InChi''' is '''International Chemical Identifier'''.

|-
| 06:19
| * It describes a chemical in terms of layers of information.

|-
| 06:25
| * Atoms and their bond connectivity,

|-
| 06:28
| * '''Isotopic, stereochemical''' and '''electronic charge''' information.

|-
| 06:34
| * For example, this is the '''InChi''' key of '''Propane'''.

|-
| 06:41
| I will clear the window.

|-
| 06:43
| Press '''Delete''' on the Keyboard.

|-
| 06:47
| To generate '''SMILES''' I will load an '''Alkaloid, Morhphine''' from the '''Templates''' menu.

|-
| 06:55
| Click on '''Tools''' Menu, then click on '''Create SMILES'''.

|-
| 07:02
| '''SMILES''' dialog box opens with '''Generated SMILES'''.

|-
| 07:07
| Dialog box contains '''SMILES''' and '''Chiral SMILES'''.

|-
| 07:13
| Click '''OK''' to close the dialog box.

|-
| 07:17
| Press '''CTRL+A''' to select the structure, if it is not selected.

|-
| 07:22
| To generate '''InChi''' key of '''Morphine''', go to '''Tools''' menu.

|-
| 07:27
| Click on '''Create InChi'''.

|-
| 07:30
| '''InChi''' dialog box opens with '''InChi generation''' of ''''Morphine''''.

|-
| 07:36
| Click '''OK''' to close the dialog box.

|-
| 07:40
| Press '''Delete''' on the keyboard to delete the '''Morphine''' structure.

|-
| 07:45
| Now we will learn to obtain a structure from inserted '''SMILES'''.

|-
| 07:50
| Below the '''Formatting''' toolbar, we have an '''Insert bar''' with an '''Insert''' button next to it.

|-
| 07:59
| Click in the '''Insert bar''' and type '''c1ccc1''' and click on '''Insert''' button.

|-
| 08:09
| '''Cyclobutene''' structure is generated on the '''Panel'''.

|-
| 08:14
| Press '''Ctrl+Z''' to undo the changes.

|-
| 08:19
| I had already saved a few '''SMILES''' and '''InChi''' keys from '''PubChem Page''' into a "Text Editor".

|-
| 08:27
| I will copy a '''SMILES''' from “Text Editor” and paste it into the '''Insert bar'''.

|-
| 08:34
| And click on '''Insert''' button.

|-
| 08:38
| Inserted '''SMILES''' displays '''Aspartic acid''' structure on the '''Panel'''.

|-
| 08:44
| Press '''Ctrl+Z''' to undo the changes.

|-
| 08:48
| I will copy an '''Inchi Key''' from the '''Text Editor''' and paste it into the '''Insert bar'''.

|-
| 08:57
| Then click on '''Insert''' button.

|-
| 09:00
| Inserted '''Inchi Key''' displays, '''Benzene''' structure onto the '''Panel'''.

|-
| 09:07
| As an assignment, insert the given '''SMILES''' and '''InChi Keys'''
to obtain various structures.

|-
| 09:16
| Let's Summarize.

|-
| 09:18
| In this tutorial, we have learnt to change,

|-
| 09:21
| * Background color of the '''Panel'''

|-
| 09:24
| * Look and feel of the window

|-
| 09:27
| * User interface language

|-
| 09:30
| * Insert '''Templates'''

|-
| 09:32
| * Generate '''SMILES''' and '''InChi keys''' for a given structure

|-
| 09:37
| * Insert '''SMILES''' and '''InChi Keys''' to generate structures

|-
| 09:43
| This video summarizes the Spoken Tutorial project.

|-
| 09:47
| If you do not have good bandwidth, you can download and watch it.

|-
| 09:52
| Spoken Tutorial Team:

|-
| 09:53
| *Conducts workshops using spoken tutorials

|-
| 09:56
| *Gives certificates to those who pass an on-line test

|-
| 09:59
| For more details, please write to '''contact@spoken-tutorial.org'''

|-
| 10:06
| Spoken Tutorial Project is a part of the Talk to a Teacher project

|-
| 10:09
| It is supported by the National Mission on Education through ICT, MHRD, Government of India

|-
| 10:17
| More information on this Mission is available at this link.

|-
| 10:23
| This is '''Madhuri Ganapathi''' from '''IIT Bombay''' signing off. Thank you for joining.
|-
|}

@@ Line 329: / Line 329: @@
 |-
 | 06:28
-| * '''Isotopic, stereochemical''' and '''electronic charge''' information.
+|  '''Isotopic, stereochemical''' and '''electronic charge''' information.
 |-

@@ Line 13: / Line 13: @@
 |-
 | 00:10
-| * Background color of the '''Panel'''
+| Background color of the '''Panel'''
 |-
 | 00:12
-| * Look and feel of the window
+| Look and feel of the window
 |-
 | 00:14
-| * User interface language.
+| User interface language.
 |-
@@ Line 29: / Line 29: @@
 |-
 | 00:20
-| * Insert '''Templates'''
+|  Insert '''Templates'''
 |-
 | 00:22
-| * Generate '''SMILES''' and '''InChi''' keys for a given structure
+|  Generate '''SMILES''' and '''InChi''' keys for a given structure
 |-
 | 00:26
-| * Insert '''SMILES''' and '''InChi''' keys to generate structures.
+|  Insert '''SMILES''' and '''InChi''' keys to generate structures.
 |-
@@ Line 45: / Line 45: @@
 |-
 | 00:33
-| * '''Ubuntu Linux''' OS version 12.04
+|  '''Ubuntu Linux''' OS version 12.04
 |-
 | 00:38
-| * '''JChemPaint''' version 3.3-1210
+|  '''JChemPaint''' version 3.3-1210
 |-
 | 00:43
-| * '''Java''' version 7
+|  '''Java''' version 7
 |-
@@ Line 301: / Line 301: @@
 |-
 | 05:45
-| * '''SMILES''' is '''simplified molecular input line entry system'''.
+|  '''SMILES''' is '''simplified molecular input line entry system'''.
 |-
 | 05:51
-| * It describes chemical structures using short '''ASCII''' strings.
+| It describes chemical structures using short '''ASCII''' strings.
 |-
 | 05:57
-| * Molecular Editors import ''''SMILES' strings''' to convert structures into 2D drawings.
+| Molecular Editors import ''''SMILES' strings''' to convert structures into 2D drawings.
 |-
@@ Line 321: / Line 321: @@
 |-
 | 06:19
-| * It describes a chemical in terms of layers of information.
+| It describes a chemical in terms of layers of information.
 |-
 | 06:25
-| * Atoms and their bond connectivity
+| Atoms and their bond connectivity
 |-
@@ Line 441: / Line 441: @@
 |-
 | 09:07
-|  As an assignment, insert the given '''SMILES''' and '''InChi Keys'''
+|  As an assignment, insert the given '''SMILES''' and '''InChi Keys''' to obtain various structures.
 to obtain various structures.
 |-
@@ Line 454: / Line 453: @@
 |-
 | 09:21
-| * Background color of the '''Panel'''
+|Background color of the '''Panel'''
 |-
 | 09:24
-| * Look and feel of the window
+| Look and feel of the window
 |-
 | 09:27
-| * User interface language
+| User interface language
 |-
 | 09:30
-| * Insert '''Templates'''
+| Insert '''Templates'''
 |-
 | 09:32
-| * Generate '''SMILES''' and '''InChi keys''' for a given structure
+| Generate '''SMILES''' and '''InChi keys''' for a given structure
 |-
 | 09:37
-| * Insert '''SMILES''' and '''InChi Keys''' to generate structures.
+| Insert '''SMILES''' and '''InChi Keys''' to generate structures.
 |-
@@ Line 486: / Line 485: @@
 |-
 | 09:52
-| Spoken Tutorial Team:
+| Spoken Tutorial Team: Conducts workshops using spoken tutorials.
-−
-|-
-| 09:53
-| * Conducts workshops using spoken tutorials.
 |-
 | 09:56
-| * Gives certificates to those who pass an on-line test.
+|  Gives certificates to those who pass an on-line test.
 |-
 | 09:59
-| For more details, please write to:
+| For more details, please write to: '''contact@spoken-tutorial.org'''
 '''contact@spoken-tutorial.org'''
 |-

@@ Line 57: / Line 57: @@
 |-
 | 00:46
-|  To follow this tutorial, you should be familiar with '''JChemPaint''' chemical structures editor.
+|  To follow this tutorial, you should be familiar with ''''JChemPaint' chemical structures editor'''.
 |-
@@ Line 73: / Line 73: @@
 |-
 | 01:10
-| Press '''Ctrl+ALt''' and '''T''' keys simultaneously  to open the '''Terminal'''.
+| Press '''Ctrl+ALt''' and 'T' keys simultaneously  to open the '''Terminal'''.
 |-
 | 01:17
-| Type: '''“cd space Desktop”''' and press '''Enter'''.
+| Type: '''cd space Desktop''' and press '''Enter'''.
 |-
 | 01:24
-| 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'''.
 |-
@@ Line 101: / Line 101: @@
 |-
 | 02:00
-|  Click on '''Choose background color''' button.
+|  Click on '''Choose Background Color''' button.
 |-
 | 02:04
-| '''Choose background color''' window opens.
+| '''Choose Background Color''' window opens.
 |-
@@ Line 145: / Line 145: @@
 |-
 | 02:55
-| Try various color combinations using '''Choose background color''' window.
+| Try various color combinations using '''Choose Background Color''' window.
 |-
@@ Line 185: / Line 185: @@
 |-
 | 03:35
-| Observe the change in look and feel of the window.
+| Observe the change in the look and feel of the window.
 |-
@@ Line 193: / Line 193: @@
 |-
 | 03:45
-| Click on '''other Preferences'''.
+| Click on '''Other Preferences'''.
 |-
 | 03:49
-| Go to '''User Interface Language''' field.
+| Go to ''''User Interface Language' field'''.
 |-
@@ Line 217: / Line 217: @@
 |-
 | 04:09
-| Click '''OK'''  button.
+| Click on '''OK'''  button.
 |-
 | 04:12
-| Observe the change in language on the '''Menu bar''' and on the '''Status bar'''.
+| Observe the change in the language on the '''Menu bar''' and on the '''Status bar'''.
 |-
@@ Line 301: / Line 301: @@
 |-
 | 05:45
-| * '''SMILES''' is simplified molecular input line entry system.
+| * '''SMILES''' is '''simplified molecular input line entry system'''.
 |-
@@ Line 309: / Line 309: @@
 |-
 | 05:57
-| * Molecular Editors import '''SMILES''' strings to convert structures into 2D drawings.
+| * Molecular Editors import ''''SMILES' strings''' to convert structures into 2D drawings.
 |-
 | 06:06
-| For example, '''CCCCCC'''  is a '''Canonical SMILES''' of '''Hexane'''
+| For example, '''CCCCCC'''  is a '''Canonical SMILES''' of '''Hexane'''.
 |-
 | 06:15
-| * '''InChi''' is '''International Chemical Identifier'''.
+| '''InChi''' is '''International Chemical Identifier'''.
 |-
@@ Line 325: / Line 325: @@
 |-
 | 06:25
-| * Atoms and their bond connectivity,
+| * Atoms and their bond connectivity
 |-
@@ Line 389: / Line 389: @@
 |-
 | 07:45
-| Now we will learn to obtain a structure from inserted '''SMILES'''.
+| Now, we will learn to obtain a structure from inserted '''SMILES'''.
 |-

@@ Line 515: / Line 515: @@
 |-
 | 10:23
-| This is '''Madhuri Ganapathi''' from '''IIT Bombay''', signing off. Thank you for joining.
+| This is Madhuri Ganapathi from '''IIT Bombay''', signing off. Thank you for joining.
 |-
 |}

@@ Line 1: / Line 1: @@
 {| border=1
-|| '''Visual Cue'''
+|| '''Time'''
 || '''Narration'''