Difference between revisions of "JChemPaint/C3/Properties-of-JChemPaint/English-timed"

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(Created page with "{|border=1 ||'''Visual Cue''' ||'''Narration''' |- | 00:00 | Hello everyone. Welcome to this tutorial on '''Properties of JChemPaint.'''. |- | 00:06 | In this tutorial, we...")
 
 
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{|border=1
 
{|border=1
||'''Visual Cue'''  
+
||'''Time'''  
 
||'''Narration'''
 
||'''Narration'''
  
 
|-
 
|-
| 00:00
+
| 00:01
 
| Hello everyone. Welcome to this tutorial on '''Properties of JChemPaint.'''.  
 
| Hello everyone. Welcome to this tutorial on '''Properties of JChemPaint.'''.  
  
 
|-
 
|-
| 00:06
+
| 00:07
| In this tutorial, we will learn  
+
| In this tutorial, we will learn:
  
 
|-
 
|-
| 00:08
+
| 00:09
| * Periodic table trends
+
| '''Periodic table''' trends
  
 
|-
 
|-
| 00:10
+
| 00:11
| * Draw a reaction and
+
| Draw a reaction and Set-up '''R-Group query'''.
  
 
|-
 
|-
| 00:12
+
| 00:16
| * Set-up '''R-Group query'''
+
| To record this tutorial, I am using:
  
 
|-
 
|-
| 00:14
+
| 00:19
| To record this tutorial I am using,
+
| '''Ubuntu Linux''' OS version '''12.04'''
  
 
|-
 
|-
| 00:17
+
| 00:23
| * '''Ubuntu Linux''' OS version 12.04
+
| '''JChemPaint''' version '''3.3-1210'''
  
 
|-
 
|-
| 00:21
+
| 00:29
| * '''JChemPaint''' version 3.3-1210
+
| '''Java''' version '''7'''.
  
 
|-
 
|-
| 00:26
+
| 00:31
| * '''Java''' version 7
+
| To follow this tutorial, you should be familiar with ''''JChemPaint' chemical structures editor'''.
  
 
|-
 
|-
| 00:29
+
| 00:39
| To follow this tutorial you should be familiar with, '''JChemPaint''' chemical structures editor.  
+
| If not, for relevant tutorials, please visit our website.
  
 
|-
 
|-
| 00:36
+
| 00:44
| * If not, for relevant tutorial,  please visit our website.
+
 
+
|-
+
| 00:41
+
 
| Let's switch to '''JChemPaint''' window.
 
| Let's switch to '''JChemPaint''' window.
  
 
|-
 
|-
| 00:45
+
| 00:48
| Recall that we had saved our '''.jar''' file on the '''Desktop'''.
+
| Recall that we had saved our ''''.jar'''' file on the '''Desktop'''.
  
 
|-
 
|-
| 00:50
+
| 00:54
| Press '''CTRl+ALt''' and '''T''' keys simultaneously  to open the '''Terminal'''.  
+
| Press '''Ctrl+ALt''' and 'T' keys simultaneously  to open the '''Terminal'''.  
  
 
|-
 
|-
| 00:55
+
| 01:00
|  Type ''''“cd space Desktop”''' and press '''Enter'''.
+
|  Type: '''cd space Desktop''' and press '''Enter'''.
  
 
|-
 
|-
| 01:02
+
| 01:06
|  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'''.
  
 
|-
 
|-
| 01:14
+
| 01:21
 
| '''JChemPaint''' window opens.
 
| '''JChemPaint''' window opens.
  
 
|-
 
|-
| 01:17
+
| 01:24
|  Let's begin with '''Periodic Table trends'''.
+
|  Let's begin with '''Periodic Table''' trends.
  
 
|-
 
|-
| 01:21
+
| 01:28
| The  '''tool bar'''  at the bottom shows buttons of some important '''elements'''.
+
| The  '''tool bar'''  at the bottom shows buttons of some important elements.
  
 
|-
 
|-
| 01:27
+
| 01:35
|  The tool bar has two extra buttons towards the right.
+
|  The tool-bar has two extra buttons towards the right.
  
 
|-
 
|-
| 01:32
+
| 01:40
| * '''Enter an element symbol via keyboard''' and
+
| '''Enter an element symbol via keyboard''' and
  
 
|-
 
|-
| 01:35
+
| 01:44
| * '''Select  new drawing symbol from periodic table'''.
+
| '''Select  new drawing symbol from periodic table'''.
  
 
|-
 
|-
| 01:40
+
| 01:48
 
|  Click on '''Select new drawing symbol from periodic table''' button.
 
|  Click on '''Select new drawing symbol from periodic table''' button.
  
 
|-
 
|-
| 01:45
+
| 01:55
 
|  '''Choose an element''' window opens with an inbuilt '''Periodic Table'''.
 
|  '''Choose an element''' window opens with an inbuilt '''Periodic Table'''.
  
 
|-
 
|-
| 01:49
+
| 02:01
|  Here we can see a box with the text '''Periodic Table of elements'''.  
+
|  Here, we can see a box with the text '''Periodic Table of elements'''.  
  
 
|-
 
|-
| 01:55
+
| 02:06
| This is an information box.
+
| This is an '''information-box'''.
  
 
|-
 
|-
| 01:57
+
| 02:11
|  The information box displays the details of chosen '''Element'''.
+
|  The information-box displays the details of chosen Element.
  
 
|-
 
|-
| 02:02
+
| 02:16
 
| For eg: I will place the cursor on '''Oxygen'''.
 
| For eg: I will place the cursor on '''Oxygen'''.
  
 
|-
 
|-
| 02:06
+
| 02:21
|  Details about '''Oxygen''' are displayed in the information box.
+
|  Details about '''Oxygen''' are displayed in the '''information-box'''.
 
   
 
   
 
|-
 
|-
| 02:10
+
| 02:26
| Likewise, we can see the details of  various  '''Elements''' in the information box.
+
| Likewise, we can see the details of  various  Elements in the information-box.
  
 
|-
 
|-
| 02:17
+
| 02:34
 
| Click on '''Close''' to close the window.
 
| Click on '''Close''' to close the window.
  
 
|-
 
|-
| 02:20
+
| 02:38
 
| Click on '''Enter an element symbol via keyboard''' button.
 
| Click on '''Enter an element symbol via keyboard''' button.
  
 
|-
 
|-
| 02:24
+
| 02:42
 
| Click on the '''Panel'''.
 
| Click on the '''Panel'''.
  
 
|-
 
|-
| 02:26
+
| 02:45
|  '''Enter element''' text box opens.
+
|  '''Enter element''' text-box opens.
  
 
|-
 
|-
| 02:28
+
| 02:48
| We can type the symbol of the '''Element''' in the text box.
+
| We can type the symbol of the Element in the text-box.
  
 
|-
 
|-
| 02:33
+
| 02:53
|  For example: I will type '''Xe''' for '''Xenon'''.
+
|  For example: I will type "Xe" for '''Xenon'''.
  
 
|-
 
|-
| 02:37
+
| 02:58
 
| Click on '''OK''' button.
 
| Click on '''OK''' button.
  
 
|-
 
|-
| 02:40
+
| 03:02
|  The symbol of '''Xenon(Xe)''' is displayed on the '''Panel'''.
+
|  The symbol of '''Xenon''' (Xe) is displayed on the '''Panel'''.
  
 
|-
 
|-
| 02:44
+
| 03:08
 
|  Now, let's draw the structure of  '''Xenondifluoride (XeF2)'''.
 
|  Now, let's draw the structure of  '''Xenondifluoride (XeF2)'''.
  
 
|-
 
|-
| 02:47
+
| 03:14
 
| Go to '''Edit''' menu, navigate to '''Preferences''' and click on it.
 
| Go to '''Edit''' menu, navigate to '''Preferences''' and click on it.
  
 
|-
 
|-
| 02:54
+
| 03:20
 
|  '''Preferences''' window opens.
 
|  '''Preferences''' window opens.
  
 
|-
 
|-
| 02:57
+
| 03:23
| Uncheck '''Show Implicit hydrogens''' check box if it is checked.
+
| Uncheck '''Show Implicit hydrogens''' check-box, if it is checked.
  
 
|-
 
|-
| 03:02
+
| 03:29
 
| Click '''OK''' to close the '''Preferences''' window.
 
| Click '''OK''' to close the '''Preferences''' window.
  
 
|-
 
|-
| 03:06
+
| 03:33
 
|  Click on '''Fluorine(F)''' button  and then click on '''Single bond'''  button.
 
|  Click on '''Fluorine(F)''' button  and then click on '''Single bond'''  button.
  
 
|-
 
|-
| 03:12
+
| 03:39
 
| Move the cursor on  '''Xenon''' atom.
 
| Move the cursor on  '''Xenon''' atom.
  
 
|-
 
|-
| 03:15
+
| 03:42
 
| Notice, a small blue circle appears on it.
 
| Notice, a small blue circle appears on it.
  
 
|-
 
|-
| 03:19
+
| 03:46
| Click and hold the left mouse button.
+
| Click and hold the '''left mouse button'''
  
 
|-
 
|-
| 03:22
+
| 03:50
| And then drag to draw two '''Xenon-Fluoride''' bonds.
+
| and then drag to draw two '''Xenon-Fluoride''' bonds.
  
 
|-
 
|-
| 03:27
+
| 03:56
| Now I will explain about '''Xenon's Atom Popup Menu'''.
+
| Now, I will explain about '''Xenon''''s '''Atom Popup Menu'''.
  
 
|-
 
|-
| 03:31
+
| 04:02
 
| Move the cursor over to '''Xenon''' atom,  right-click on it.
 
| Move the cursor over to '''Xenon''' atom,  right-click on it.
  
 
|-
 
|-
| 03:36
+
| 04:07
| '''Xenon's Atom Popup Menu''' opens.
+
| '''Xenon''''s '''Atom Popup Menu''' opens.
  
 
|-
 
|-
| 03:40
+
| 04:11
| Here, I will explain about  '''Isotopes, Change Element''' and '''Properties''' options.  
+
| Here, I will explain about  '''Isotopes, Change Element''' and '''Molecular Properties''' options.  
  
 
|-
 
|-
| 03:46
+
| 04:18
 
|  Let's first move to '''Isotopes'''.
 
|  Let's first move to '''Isotopes'''.
  
 
|-
 
|-
| 03:49
+
| 04:21
| A submenu opens with a list of '''Isotopes of Xenon'''.
+
| A sub-menu opens with a list of isotopes of Xenon.
  
 
|-
 
|-
| 03:54
+
| 04:26
 
| Next, I will move the cursor to '''Change Element'''.
 
| Next, I will move the cursor to '''Change Element'''.
  
 
|-
 
|-
| 03:58
+
| 04:30
| A submenu opens with various categories of  '''elements'''.  
+
| A sub-menu opens with various categories of  elements.  
  
 
|-
 
|-
| 04:02
+
| 04:36
| I will scroll down to various categories.  
+
| I will scroll-down to various categories.  
  
 
|-
 
|-
| 04:06
+
| 04:40
 
| I will choose '''Alkali Earth Metals'''.  
 
| I will choose '''Alkali Earth Metals'''.  
  
 
|-
 
|-
| 04:09
+
| 04:44
 
| '''Alkali Earth Metals''' list opens.
 
| '''Alkali Earth Metals''' list opens.
  
 
|-
 
|-
| 04:12
+
| 04:48
 
| Select '''Calcium(Ca)''' from the list.
 
| Select '''Calcium(Ca)''' from the list.
  
 
|-
 
|-
| 04:15
+
| 04:52
| We see that '''element Xenon''' is replaced by '''Calcium'''.
+
| We see that element '''Xenon''' is replaced by '''Calcium'''.
  
 
|-
 
|-
| 04:19
+
| 04:57
 
| Now, we move on to '''Molecular Properties''' option.
 
| Now, we move on to '''Molecular Properties''' option.
  
 
|-
 
|-
| 04:23
+
| 05:01
| Right click on '''Calcium'''.
+
| Right-click on '''Calcium'''.
  
 
|-
 
|-
| 04:26
+
| 05:04
| '''Calcium's Atom Popup Menu''' opens.
+
| '''Calcium''''s '''Atom Popup Menu''' opens.
  
 
|-
 
|-
| 04:29
+
| 05:08
 
| Click on '''Molecular Properties''' option.
 
| Click on '''Molecular Properties''' option.
  
 
|-
 
|-
| 04:33
+
| 05:11
| '''Properties''' text box opens.
+
| '''Properties''' text-box opens.
  
 
|-
 
|-
| 04:36
+
| 05:14
| Type the name of the compound as '''Calcium Fluoride''' and click on '''OK''' button.
+
| Type the name of the compound as "Calcium Fluoride" and click on '''OK''' button.
  
 
|-
 
|-
| 04:43
+
| 05:20
 
| Name of the compound is displayed below the structure.
 
| Name of the compound is displayed below the structure.
  
 
|-
 
|-
| 04:47
+
| 05:24
 
|  Let us save the file now.
 
|  Let us save the file now.
  
 
|-
 
|-
| 04:49
+
| 05:26
| Click on '''Save''' button on the tool bar.
+
| Click on '''Save''' button on the tool-bar.
  
 
|-
 
|-
| 04:53
+
| 05:30
| '''Save''' dialog box opens.  
+
| '''Save''' dialog-box opens.  
  
 
|-
 
|-
| 04:56
+
| 05:32
| Type the file name as '''Calcium-fluoride'''.
+
| Type the file name as "Calcium-fluoride".
  
 
|-
 
|-
| 05:00
+
| 05:36
 
| Click on '''Save''' button.
 
| Click on '''Save''' button.
  
 
|-
 
|-
| 05:03
+
| 05:39
 
|  Next, we will learn how to create a reaction.
 
|  Next, we will learn how to create a reaction.
  
 
|-
 
|-
| 05:06
+
| 05:42
 
| To draw a reaction, we need to draw the required structures.
 
| To draw a reaction, we need to draw the required structures.
  
 
|-
 
|-
| 05:10
+
| 05:48
 
| I have opened a new window with required structures.
 
| I have opened a new window with required structures.
  
 
|-
 
|-
| 05:14
+
| 05:52
| Here the reactants are '''Propene''' and '''Chlorine''' molecules and product is '''1,2-dicholoropropane'''.
+
| Here, the reactants are '''Propene''' and '''Chlorine''' molecules and product is '''1,2-dicholoropropane'''.
  
 
|-
 
|-
| 05:23
+
| 06:01
| On the left side tool bar, click on the '''Reaction arrow''' button.
+
| On the left side tool bar, click on the '''Reaction Arrow''' button.
  
 
|-
 
|-
| 05:27
+
| 06:06
 
| Click between reactants and products.
 
| Click between reactants and products.
  
 
|-
 
|-
| 05:31
+
| 06:10
 
| The reaction is created.
 
| The reaction is created.
  
 
|-
 
|-
| 05:33
+
| 06:13
| We will now allign the structures properly in the reaction.
+
| We will now align the structures properly in the reaction.
 
   
 
   
 
|-
 
|-
| 05:37
+
| 06:18
| Click on '''Relayout the structures''' button on the top tool bar.
+
| Click on '''Relayout the structures''' button on the top tool bar. Structures align properly.
  
 
|-
 
|-
| 05:42
+
| 06:27
|  I will now discuss about how to set up an '''R group query'''.
+
|  I will now discuss about how to set up an '''R-group query'''.
  
 
|-
 
|-
| 05:47
+
| 06:31
 
|  What is an '''R-group query'''?
 
|  What is an '''R-group query'''?
  
 
|-
 
|-
| 05:50
+
| 06:35
| * An '''R-group query''' involves  '''Root structure''' and '''substituents'''.
+
| An '''R-group query''' involves  '''Root structure''' and '''substituents'''.
  
 
|-
 
|-
| 05:55
+
| 06:41
| * It  represents substitution on the same '''root structure'''.
+
| It  represents substitution on the same '''Root structure'''.
  
 
|-
 
|-
| 06:00
+
| 06:45
| * It can involve derivatives which differ in one or more substituents.
+
| It can involve derivatives which differ in one or more substituents.
  
 
|-
 
|-
| 06:06
+
| 06:53
 
| Click on '''Create a new file''' icon to open a new window.
 
| Click on '''Create a new file''' icon to open a new window.
  
 
|-
 
|-
| 06:11
+
| 07:01
 
| Click on '''Draw a chain''' button.
 
| Click on '''Draw a chain''' button.
  
 
|-
 
|-
| 06:14
+
| 07:03
| Click on the '''Panel''' to draw a '''Carbon''' chain  with three '''Carbon''' atoms.
+
| Click on the '''Panel''' to draw a Carbon chain  with three Carbon atoms.
  
 
|-
 
|-
| 06:20
+
| 07:09
 
| Let's create a substituent that has to be attached to the '''Carbon''' chain.  
 
| Let's create a substituent that has to be attached to the '''Carbon''' chain.  
  
 
|-
 
|-
| 06:24
+
| 07:14
 
| For example, '''Benzene'''.
 
| For example, '''Benzene'''.
  
 
|-
 
|-
| 06:27
+
| 07:17
| Click on '''Benzene''' ring on right side tool bar.  
+
| Click on '''Benzene ring''' on right side tool bar.  
  
 
|-
 
|-
| 06:30
+
| 07:22
| Click on the '''Panel'''.  
+
| Click on the Panel.  
  
 
|-
 
|-
| 06:33
+
| 07:24
|  Let's label the terminal '''Carbon''' atom as  '''R1''' in the '''Carbon''' chain.
+
|  Let's label the terminal '''Carbon''' atom as  'R1' in the '''Carbon''' chain.
  
 
|-
 
|-
| 06:39
+
| 07:31
| Right click on terminal '''Carbon''' atom.
+
| Right-click on terminal '''Carbon''' atom.
  
 
|-
 
|-
| 06:42
+
| 07:35
| '''Atom Pop menu''' opens.
+
| '''Atom Popup menu''' opens.
  
 
|-
 
|-
| 06:45
+
| 07:38
 
| Scroll down to '''Pseudo Atoms'''.
 
| Scroll down to '''Pseudo Atoms'''.
  
 
|-
 
|-
| 06:48
+
| 07:42
| A submenu opens; select '''R1'''.
+
| A sub-menu opens; select 'R1'.
  
 
|-
 
|-
| 06:52
+
| 07:45
 
| Now let's define the '''Carbon''' chain as '''root structure'''.
 
| Now let's define the '''Carbon''' chain as '''root structure'''.
  
 
|-
 
|-
| 06:56
+
| 07:50
 
| Click on '''Selection''' button.
 
| Click on '''Selection''' button.
  
 
|-
 
|-
| 06:58
+
| 07:53
 
| Select the '''Root structure''' by dragging over it.
 
| Select the '''Root structure''' by dragging over it.
  
 
|-
 
|-
| 07:02
+
| 07:57
 
|  Go to '''R-groups''' menu and select '''Define as Root Structure'''.  
 
|  Go to '''R-groups''' menu and select '''Define as Root Structure'''.  
  
 
|-
 
|-
| 07:09
+
| 08:04
 
| The substituent structure will be added as  '''Not in R-Group'''.
 
| The substituent structure will be added as  '''Not in R-Group'''.
  
 
|-
 
|-
| 07:14
+
| 08:10
 
| Click on '''Selection''' button;
 
| Click on '''Selection''' button;
  
 
|-
 
|-
| 07:17
+
| 08:13
 
|  select the '''Substituent'''.
 
|  select the '''Substituent'''.
  
 
|-
 
|-
| 07:19
+
| 08:16
 
| Go to '''R-groups''' menu and select '''Define as Substituent'''.
 
| Go to '''R-groups''' menu and select '''Define as Substituent'''.
  
 
|-
 
|-
| 07:26
+
| 08:22
|  An input box opens.
+
|  An '''input-box''' opens.
  
 
|-
 
|-
| 07:27
+
| 08:24
| Here, enter an '''R-group''' number as “1” and click on '''OK''' button.
+
| Here, enter '''R-group''' number as “1” and click on '''OK''' button.
  
 
|-
 
|-
| 07:34
+
| 08:30
| The substituent will be numbered as '''R1'''.
+
| The substituent will be numbered as 'R1'.
  
 
|-
 
|-
| 07:38
+
| 08:34
|  On the '''Root structure,''' the substituent '''R1''' will be marked as asterisk(*)
+
|  On the '''Root structure,''' the substituent 'R1' will be marked with an asterisk(*)
  
 
|-
 
|-
| 07:44
+
| 08:41
| The attaching '''Carbon''' atom of the substituent '''R1''' will also be marked with an asterisk(*).
+
| The attaching '''Carbon''' atom of the substituent 'R1' will also be marked with an asterisk(*).
  
 
|-
 
|-
| 07:51
+
| 08:49
 
| Click on the '''Selection''' button,  select  '''Root Structure''' and  '''substituent(R1)'''.
 
| Click on the '''Selection''' button,  select  '''Root Structure''' and  '''substituent(R1)'''.
  
 
|-
 
|-
| 07:58
+
| 08:56
 
|  Go to '''R-groups''' menu,  select '''General Possible configurations(sdf)'''.
 
|  Go to '''R-groups''' menu,  select '''General Possible configurations(sdf)'''.
  
 
|-
 
|-
| 08:05
+
| 09:03
| '''Save''' dialog box opens.
+
| '''Save''' dialog-box opens.
  
 
|-
 
|-
| 08:08
+
| 09:06
| Type the file name as '''r-group''',  select the location as '''Desktop'''.
+
| Type the file name as "r-group",  select the location as Desktop.
  
 
|-
 
|-
| 08:14
+
| 09:12
 
| Click on '''Save''' button.
 
| Click on '''Save''' button.
  
 
|-
 
|-
| 08:18
+
| 09:15
 
| Click on '''Open''' icon on the tool bar.
 
| Click on '''Open''' icon on the tool bar.
 
    
 
    
 
|-
 
|-
| 08:21
+
| 09:19
| '''Open''' dialogue box opens.
+
| '''Open''' dialogue-box opens.
  
 
|-
 
|-
| 08:24
+
| 09:22
| In the “Files of Type”,  select “All Files”
+
| In the “Files of Type”,  select “All Files”.
  
 
|-
 
|-
| 08:28
+
| 09:27
 
| Click on '''Desktop'''.
 
| Click on '''Desktop'''.
  
 
|-
 
|-
| 08:30
+
| 09:29
| Click '''Open'''; then select the saved '''r-group''' file.
+
| Click '''Open'''; then select the saved "r-group" file.
  
 
|-
 
|-
| 08:36
+
| 09:34
| Click on “Open” button.
+
| Click on '''Open''' button.
  
 
|-
 
|-
| 08:39
+
| 09:37
 
| A message pops up; click '''OK'''.
 
| A message pops up; click '''OK'''.
  
 
|-
 
|-
| 08:43
+
| 09:41
 
| A new file opens with '''r-group query''' structure.
 
| A new file opens with '''r-group query''' structure.
  
 
|-
 
|-
| 08:48
+
| 09:46
| To allign the structure properly, click on '''Relayout the structure''' button  on the tool bar.
+
| To align the structure properly, click on '''Relayout the structure''' button  on the tool bar.
  
 
|-
 
|-
| 08:55
+
| 09:54
 
| The structure shown is '''root structure''' along with attached '''R-group substituent  Benzene'''.  
 
| The structure shown is '''root structure''' along with attached '''R-group substituent  Benzene'''.  
  
 
|-
 
|-
| 09:02
+
| 10:02
 
| Let's summarize.
 
| Let's summarize.
  
 
|-
 
|-
| 09:03
+
| 10:04
| In this tutorial we have learnt
+
| In this tutorial, we have learnt:
  
 
|-
 
|-
| 09:05
+
| 10:06
| * Periodic table trends
+
| '''Periodic table''' trends
  
 
|-
 
|-
| 09:07
+
| 10:09
| * Draw a reaction
+
| Draw a reaction
  
 
|-
 
|-
| 09:08
+
| 10:11
| * Set up '''R-Group query'''.
+
| Set up '''R-Group query'''.
  
 
|-
 
|-
| 09:11
+
| 10:14
| As an assignment,
+
| As an assignment-
  
 
|-
 
|-
| 09:12
+
| 10:16
| * Explore various Periodic table trends and
+
| Explore various Periodic table trends and
  
 
|-
 
|-
| 09:16
+
| 10:19
| * Draw reactions of your choice.
+
| Draw reactions of your choice.
  
 
|-
 
|-
| 09:19
+
| 10:24
| This video summarizes the Spoken Tutorial project
+
| This video summarizes the Spoken Tutorial project.
  
 
|-
 
|-
| 09:23
+
| 10:28
 
| 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.   
  
 
|-
 
|-
| 09:28
+
| 10:33
|  Spoken Tutorial team conducts workshops using Spoken Tutorials  and gives certificates.
+
|  Spoken Tutorial team conducts workshops using '''Spoken Tutorials''' and gives certificates.
  
 
|-
 
|-
| 09:34
+
| 10:39
 
| Please contact us.
 
| Please contact us.
  
 
|-
 
|-
| 09:37
+
| 10:42
| The Spoken Tutorial Project is funded by '''NMEICT, MHRD Government of India'''.
+
| The Spoken Tutorial project is funded by NMEICT, MHRD Government of India.
 
    
 
    
 
|-
 
|-
| 09:44
+
| 10:49
| More information on this Mission is available at this link.
+
| More information on this mission is available at this link.
  
 
|-
 
|-
| 09:49
+
| 10:55
| 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.  
|-
+
 
 
|}
 
|}

Latest revision as of 17:13, 9 March 2017

Time Narration
00:01 Hello everyone. Welcome to this tutorial on Properties of JChemPaint..
00:07 In this tutorial, we will learn:
00:09 Periodic table trends
00:11 Draw a reaction and Set-up R-Group query.
00:16 To record this tutorial, I am using:
00:19 Ubuntu Linux OS version 12.04
00:23 JChemPaint version 3.3-1210
00:29 Java version 7.
00:31 To follow this tutorial, you should be familiar with 'JChemPaint' chemical structures editor.
00:39 If not, for relevant tutorials, please visit our website.
00:44 Let's switch to JChemPaint window.
00:48 Recall that we had saved our '.jar' file on the Desktop.
00:54 Press Ctrl+ALt and 'T' keys simultaneously to open the Terminal.
01:00 Type: cd space Desktop and press Enter.
01:06 Type: java space -jar space ./jchempaint-3.3-1210.jar and press Enter.
01:21 JChemPaint window opens.
01:24 Let's begin with Periodic Table trends.
01:28 The tool bar at the bottom shows buttons of some important elements.
01:35 The tool-bar has two extra buttons towards the right.
01:40 Enter an element symbol via keyboard and
01:44 Select new drawing symbol from periodic table.
01:48 Click on Select new drawing symbol from periodic table button.
01:55 Choose an element window opens with an inbuilt Periodic Table.
02:01 Here, we can see a box with the text Periodic Table of elements.
02:06 This is an information-box.
02:11 The information-box displays the details of chosen Element.
02:16 For eg: I will place the cursor on Oxygen.
02:21 Details about Oxygen are displayed in the information-box.
02:26 Likewise, we can see the details of various Elements in the information-box.
02:34 Click on Close to close the window.
02:38 Click on Enter an element symbol via keyboard button.
02:42 Click on the Panel.
02:45 Enter element text-box opens.
02:48 We can type the symbol of the Element in the text-box.
02:53 For example: I will type "Xe" for Xenon.
02:58 Click on OK button.
03:02 The symbol of Xenon (Xe) is displayed on the Panel.
03:08 Now, let's draw the structure of Xenondifluoride (XeF2).
03:14 Go to Edit menu, navigate to Preferences and click on it.
03:20 Preferences window opens.
03:23 Uncheck Show Implicit hydrogens check-box, if it is checked.
03:29 Click OK to close the Preferences window.
03:33 Click on Fluorine(F) button and then click on Single bond button.
03:39 Move the cursor on Xenon atom.
03:42 Notice, a small blue circle appears on it.
03:46 Click and hold the left mouse button
03:50 and then drag to draw two Xenon-Fluoride bonds.
03:56 Now, I will explain about Xenon's Atom Popup Menu.
04:02 Move the cursor over to Xenon atom, right-click on it.
04:07 Xenon's Atom Popup Menu opens.
04:11 Here, I will explain about Isotopes, Change Element and Molecular Properties options.
04:18 Let's first move to Isotopes.
04:21 A sub-menu opens with a list of isotopes of Xenon.
04:26 Next, I will move the cursor to Change Element.
04:30 A sub-menu opens with various categories of elements.
04:36 I will scroll-down to various categories.
04:40 I will choose Alkali Earth Metals.
04:44 Alkali Earth Metals list opens.
04:48 Select Calcium(Ca) from the list.
04:52 We see that element Xenon is replaced by Calcium.
04:57 Now, we move on to Molecular Properties option.
05:01 Right-click on Calcium.
05:04 Calcium's Atom Popup Menu opens.
05:08 Click on Molecular Properties option.
05:11 Properties text-box opens.
05:14 Type the name of the compound as "Calcium Fluoride" and click on OK button.
05:20 Name of the compound is displayed below the structure.
05:24 Let us save the file now.
05:26 Click on Save button on the tool-bar.
05:30 Save dialog-box opens.
05:32 Type the file name as "Calcium-fluoride".
05:36 Click on Save button.
05:39 Next, we will learn how to create a reaction.
05:42 To draw a reaction, we need to draw the required structures.
05:48 I have opened a new window with required structures.
05:52 Here, the reactants are Propene and Chlorine molecules and product is 1,2-dicholoropropane.
06:01 On the left side tool bar, click on the Reaction Arrow button.
06:06 Click between reactants and products.
06:10 The reaction is created.
06:13 We will now align the structures properly in the reaction.
06:18 Click on Relayout the structures button on the top tool bar. Structures align properly.
06:27 I will now discuss about how to set up an R-group query.
06:31 What is an R-group query?
06:35 An R-group query involves Root structure and substituents.
06:41 It represents substitution on the same Root structure.
06:45 It can involve derivatives which differ in one or more substituents.
06:53 Click on Create a new file icon to open a new window.
07:01 Click on Draw a chain button.
07:03 Click on the Panel to draw a Carbon chain with three Carbon atoms.
07:09 Let's create a substituent that has to be attached to the Carbon chain.
07:14 For example, Benzene.
07:17 Click on Benzene ring on right side tool bar.
07:22 Click on the Panel.
07:24 Let's label the terminal Carbon atom as 'R1' in the Carbon chain.
07:31 Right-click on terminal Carbon atom.
07:35 Atom Popup menu opens.
07:38 Scroll down to Pseudo Atoms.
07:42 A sub-menu opens; select 'R1'.
07:45 Now let's define the Carbon chain as root structure.
07:50 Click on Selection button.
07:53 Select the Root structure by dragging over it.
07:57 Go to R-groups menu and select Define as Root Structure.
08:04 The substituent structure will be added as Not in R-Group.
08:10 Click on Selection button;
08:13 select the Substituent.
08:16 Go to R-groups menu and select Define as Substituent.
08:22 An input-box opens.
08:24 Here, enter R-group number as “1” and click on OK button.
08:30 The substituent will be numbered as 'R1'.
08:34 On the Root structure, the substituent 'R1' will be marked with an asterisk(*)
08:41 The attaching Carbon atom of the substituent 'R1' will also be marked with an asterisk(*).
08:49 Click on the Selection button, select Root Structure and substituent(R1).
08:56 Go to R-groups menu, select General Possible configurations(sdf).
09:03 Save dialog-box opens.
09:06 Type the file name as "r-group", select the location as Desktop.
09:12 Click on Save button.
09:15 Click on Open icon on the tool bar.
09:19 Open dialogue-box opens.
09:22 In the “Files of Type”, select “All Files”.
09:27 Click on Desktop.
09:29 Click Open; then select the saved "r-group" file.
09:34 Click on Open button.
09:37 A message pops up; click OK.
09:41 A new file opens with r-group query structure.
09:46 To align the structure properly, click on Relayout the structure button on the tool bar.
09:54 The structure shown is root structure along with attached R-group substituent Benzene.
10:02 Let's summarize.
10:04 In this tutorial, we have learnt:
10:06 Periodic table trends
10:09 Draw a reaction
10:11 Set up R-Group query.
10:14 As an assignment-
10:16 Explore various Periodic table trends and
10:19 Draw reactions of your choice.
10:24 This video summarizes the Spoken Tutorial project.
10:28 If you do not have good bandwidth, you can download and watch it.
10:33 Spoken Tutorial team conducts workshops using Spoken Tutorials and gives certificates.
10:39 Please contact us.
10:42 The Spoken Tutorial project is funded by NMEICT, MHRD Government of India.
10:49 More information on this mission is available at this link.
10:55 This is Madhuri Ganapathi from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

Gaurav, PoojaMoolya, Pratik kamble, Ranjana, Sandhya.np14