JChemPaint/C3/Properties-of-JChemPaint/English - Revision history

PoojaMoolya at 09:56, 28 October 2020

2020-10-28T09:56:59Z

Nancyvarkey at 07:32, 7 January 2015

2015-01-07T07:32:17Z

Madhurig: Created page with "{| border=1 || '''Visual Cue''' || '''Narration''' |- ||'''Slide Number 1 Title Slide''' ||Hello everyone. Welcome to this tutorial on '''Properties of JChemPaint.'''. |-..."

2015-01-06T12:58:39Z

Created page with "{| border=1 || '''Visual Cue''' || '''Narration''' |- ||'''Slide Number 1 Title Slide''' ||Hello everyone. Welcome to this tutorial on '''Properties of JChemPaint.'''. |-..."

New page

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
||'''Slide Number 1

Title Slide'''
||Hello everyone.

Welcome to this tutorial on '''Properties of JChemPaint.'''.
|-
||'''Slide Number 2

Learning Objectives'''
|| In this tutorial, we will learn to change

* Periodic table trends

* Draw a reaction and

* Set-up R-Group query
|-
||'''Slide Number 3

System Requirement'''
||To record this tutorial I am using,

* '''Ubuntu Linux''' OS version 12.04

* '''JChemPaint''' version 3.3-1210

* '''Java''' version 7
|-
||'''Slide Number 4

Pre-requisites'''
|| To follow this tutorial you should be familiar with,

* '''JChemPaint''' chemical structures editor.

* If not, for relevant tutorial, please visit our website.
|-
||
||Let's switch to '''JChemPaint''' window.
|-
||Point to '''.jar''' file
||Recall that we had saved our '''.jar''' file on the '''Desktop'''.
|-
||Press '''CTRl+ALt+T''' keys simultaneously to open the terminal.
||Press '''CTRl+ALt''' and '''T''' keys simultaneously to open the '''Terminal'''.
|-
||Type '''“cd space Desktop”''' and press enter.

Type '''java -jar ./jchempaint-3.3-1210.jar''' and press enter.
||Type ''''“cd space Desktop”''' and press enter.

Type ''' “java space -jar space ./jchempaint-3.3-1210.jar”''' and press enter.

'''JChemPaint''' window opens.
|-
||
||Let's begin with '''Periodic Table trends'''.
|-
||Point to the '''Tool bar''' at the bottom.

Point to the element buttons.
|| The '''tool bar''' at the bottom shows buttons of some important '''elements'''.
|-
||Point to the buttons.
|| The tool bar has two extra buttons towards the right.

* '''Enter an element symbol via keyboard''' and

* '''Select new drawing symbol from periodic table'''.
|-
||Click on the button.
|| Click on '''Select new drawing symbol from periodic table''' button.
|-
|| Move the cursor towards the window.
|| '''Choose an element''' window opens with an inbuilt '''Periodic Table'''.
|-
||Point to information box.
||Here we can see a box with the text '''Periodic Table of elements'''.

This is an information box.
|-
||Point to information box.

Move the cursor on to '''Oxygen'''.
||The information box displays the details of the chosen '''Element'''.

For eg: I will place the cursor on '''Oxygen'''.
|-
||Point to the information box.

Point to different elements.
||Details about '''Oxygen''' are displayed in the information box.

Likewise, we can see the details of various '''Elements''' in the information box.
|-
||Click on '''Close'''.
||Click on '''Close''' to close the window.
|-
||Click on '''Enter an element symbol via keyboard''' button >> click on the '''Panel'''.
||Click on '''Enter an element symbol via keyboard''' button.

Click on the '''Panel'''.
|-
||Point to the box.
||'''Enter element''' text box opens.

We can type the symbol of the '''Element''' in the text box.
|-
||Type '''Xe''' for '''Xenon''' in the box >> click on '''OK''' button.
||For example: I will type '''Xe''' for '''Xenon'''.

Click on '''OK''' button.
|-
||Point to the symbol.
|| The symbol of '''Xenon(Xe)''' is displayed on the '''Panel'''.
|-
||
||Now, let's draw the structure of '''Xenondifluoride (XeF2)'''.
|-
||Go to '''Edit''' menu and navigate to '''Preferences'''>> click on it.
||Go to '''Edit''' menu, navigate to '''Preferences''' and click on it.
|-
||Point to the '''Preferences''' window
||'''Preferences''' window opens.
|-
||Point to '''Show Implicit hydrogens''' check box.

Click Ok to close the Preferences window.
||Uncheck '''Show Implicit hydrogens''' check box if it is checked.

Click '''OK''' to close the '''Preferences''' window.
|-
|| Click on '''Fluorine(F)''' button >> click on '''Single bond''' button.
||Click on '''Fluorine(F)''' button and then click on '''Single bond''' button.
|-
||Move the cursor on '''Xenon''' atom.

Point to the blue circle.
||Move the cursor on '''Xenon''' atom.

Notice, a small blue circle appears on it.
|-
||Click >> hold the left mouse button.
||Click and hold the left mouse button.

And then drag to draw two '''Xenon-Fluoride''' bonds.
|-
||
||Now I will explain about '''Xenon's Atom Popup Menu'''.
|-
||Right click on '''Xenon'''.

Point to '''Atom Popup Menu'''.
||Move the cursor over to '''Xenon''' atom, right-click on it.

'''Xenon's Atom Popup Menu''' opens.
|-
||Point to '''Isotopes, Change Element''' and '''Properties'''.
||Here, I will explain about '''Isotopes, Change Element''' and '''Properties''' options.
|-
||Point to the submenu >>'''Isotopes of Xenon'''.
|| Let's first move to '''Isotopes'''.

A submenu opens with a list of '''Isotopes of Xenon'''.
|-
||Move the cursor to '''Change Element'''.
|| Next, I will move the cursor to '''Change Element'''.
|-
||Point to the submenu >>various categories of elements of elements.
||A submenu opens with various categories of '''elements'''.

I will scroll down to various categories.
|-
||Move the cursor to '''Alkali Earth Metals'''.

Point to the list.
||I will choose '''Alkali Earth Metals'''.

'''Alkali Earth Metals''' list opens.
|-
||Select the '''Calcium''' from the list.

Point to the replaced element.
||Select '''Calcium(Ca)''' from the list.

We see that '''element Xenon''' is replaced by '''Calcium'''.
|-
||Right click on '''Calcium'''.

'''Calcium's Atom Popup Menu''' opens.
||Now, we move on to '''Molecular Properties''' option.

Right click on '''Calcium'''.

'''Calcium's Atom Popup Menu''' opens.
|-
||Move the cursor to '''Molecular Properties''' option.

Point to '''Properties''' text box.

||Click on '''Molecular Properties''' option.

'''Properties''' text box opens.
|-
||Type compound's name.

Point to the displayed text.
||Type the name of the compound as '''Calcium Fluoride''' and click '''OK''' button.

Name of the compound is displayed below the structure.
|-
||Click on '''Save''' button the tool bar.
|| Let's save the file now.

Click on '''Save''' button on the tool bar.
|-
||Point to the dialogue box.
||'''Save''' dialogue box opens.
|-
||Type the file name as '''Calcium-fluoride'''.

Click on '''Save''' button.
||Type the file name as '''Calcium-fluoride'''.

Click on '''Save''' button.
|-
||
|| Next, we will learn how to create a reaction.
|-
||
||To draw a reaction, we need to draw the required structures.
|-
||Point to the window.

Point to the reactants and products.
||I have opened a new window with required structures.

Here the reactants are '''Propene''' and '''Chlorine''' molecules and product is '''1,2-dicholoropropane'''.
|-
||Click on Reaction arrow button.

Click between reactants and products.

Point to the created reaction.
||On the left side tool bar, click on the '''Reaction arrow''' button.

Click between reactants and products.

The reaction is created.
|-
||Click on '''Relayout the structures''' button on the tool bar.
||We will now allign the structures properly in the reaction.

Click on '''Relayout the structures''' button on the top tool bar.
|-
||
|| I will now discuss about how to set up an '''R group query'''.
|-
||'''Slide Number 5

R-group query'''
|| What is an '''R-group query'''?

* An '''R-group query''' involves '''Root structure''' and '''substituents'''.

* It represents substitution on the same '''root structure'''.

* It can involve derivatives which differ in one or more substituents.
|-
||Click on '''Create a new file''' icon.
||Click on '''Create a new file''' icon to open a new window.
|-
||Click on '''Draw a chain''' button.

Click on the '''Panel''' >> drag to draw a '''Carbon''' chain with three '''Carbons'''.
||Click on '''Draw a chain''' button.

Click on the '''Panel''' and drag to draw a '''Carbon''' chain with three '''Carbon''' atoms.
|-
||
||Let's create a substituent that has to be attached to the '''Carbon''' chain.

For example, '''Benzene'''.
|-
||Click on '''Benzene''' ring on right side tool bar.

Click on the '''Panel'''.
||Click on '''Benzene''' ring on right side tool bar.

Click on the '''Panel'''.
|-
||Point to the terminal '''Carbon''' atom
|| Let's label the terminal '''Carbon''' atom as '''R1''' in the '''Carbon''' chain.
|-
||Right click on terminal '''Carbon''' atom.

Move the cursor onto '''Atom Pop menu'''.
||Right click on terminal '''Carbon''' atom.

'''Atom Pop menu''' opens.
|-
||Point to the submenu.
||Scroll down to '''Pseudo Atoms'''.

A submenu opens select '''R1'''.
|-
||
||Now let's define the '''Carbon''' chain as '''root structure'''.
|-
||Click on '''Selection''' button.
||Click on '''Selection''' button.

Select the '''Root structure''' by dragging over it.
|-
||Go to '''R-groups''' menu and select '''Define as Root Structure'''.

Point to the substituents.

|| Go to '''R-groups''' menu and select '''Define as Root Structure'''.

The substituent structure will be added as '''Not in R-Group'''.

|-
||Click on '''Select''' button and select the Substituent.

Go to '''R-groups''' menu and select '''Define as Substituent'''.
||Click on '''Selection''' button, select the '''Substituent'''.

Go to '''R-groups''' menu and select '''Define as Substituent'''.
|-
||Point to the input box.

Point to the substituent.
|| An input box opens.

Here enter an '''R-group''' number as “1” and click '''OK''' button.

The substituent will be numbered as '''R1'''.
|-
||Point to the '''Root structure''' marked as asterisk(*)

Point to the substituent marked with asterisk(*)
|| On the '''Root structure''' the substituent '''R1''' will be marked as asterisk(*)

The attaching '''Carbon''' atom of the substituent '''R1''' will also be marked with an asterisk(*)
|-
||Click on '''Selection''' button>> select '''Root Structure''' and '''substituent(R1)'''.
||Click on the '''Selection''' button, select the '''Root Structure''' and '''substituent(R1)'''.
|-
||Go to '''R-groups''' menu>> select '''General Possible configurations(sdf)'''.
|| Go to '''R-groups''' menu, select '''General Possible configurations(sdf)'''.
|-
||Point to the dialogue box.
||'''Save''' dialogue box opens.
|-
||Type the file name as '''r-group''' >>select the file location as '''Desktop'''.

Click on '''Save''' button.
||Type the file name as '''r-group''', select the file location as '''Desktop'''.

Click on '''Save''' button.
|-
||Click on '''Open''' icon on the tool bar
||Click on '''Open''' icon on the tool bar.

'''Open''' dialogue box opens.
|-
||Point to “Files of Type” field select “All Files”.
||In the “Files of Type”, select “All Files”
|-
||Click on '''Desktop''' folder>>select the saved '''r-group''' file.

Click on “Open”
||Click on '''Desktop''' folder.

Click '''Open''' then select the saved '''r-group''' file.

Click on “Open” button.
|-
||Point to OK
||A message pops up, click '''OK'''.
|-
||Move the cursor on the file.
||A new file opens with '''r-group query''' structure.
|-
||Click on '''Relayout the structures''' button on the tool bar.
||To allign the structure properly,

Click on '''Relayout the structure''' button on the tool bar.
|-
||Point to the structure.
||The structure shown is '''root structure''' along with attached '''R-group substituent Benzene'''.
|-
||
||Let's summarize.
|-
||'''Slide Number 6

Summary'''
||In this tutorial we have learnt

* Periodic table trends

* Draw a reaction

* Set up R-Group query.
|-
||'''Slide Number 7

Assignment'''.
||As an assignment,

* Explore various Periodic table trends and

* Draw reactions of your choice.
|-
||'''Slide Number8'''
'''Acknowledgement'''
||This video summarizes the Spoken Tutorial project

If you do not have good bandwidth, you can download and watch it.
|-
||'''Slide Number 9'''
|| Spoken Tutorial team conducts workshops using Spoken Tutorials and gives certificates.

Please contact us.
|-
||'''Slide number 10'''
||The Spoken Tutorial Project is funded by '''NMEICT, MHRD Government of India'''.

More information on this Mission is available at this link.
'''http://spoken-tutorial.org/NMEICT-Intro ]'''

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

@@ Line 221: / Line 221: @@
 Click on '''Save''' button on the tool bar.
 |-
-||Point to the dialogue box.
+||Point to the dialog box.
 ||'''Save''' dialog box opens.
 |-
@@ Line 370: / Line 370: @@
 ||Click on '''Open''' icon on the tool bar.
-'''Open''' dialogue box opens.
+'''Open''' dialog box opens.
 |-
 ||Point to “Files of Type”  field select “All Files”.

@@ Line 19: / Line 19: @@
 * Draw a reaction and
-* Set-up R-Group query
+* Set-up '''R-Group query'''
 |-
 ||'''Slide Number 3
@@ Line 50: / Line 50: @@
 ||Press '''CTRl+ALt''' and '''T''' keys simultaneously  to open the '''Terminal'''.
 |-
-||Type '''“cd space Desktop”''' and press enter.
+||Type '''“cd space Desktop”''' and press '''Enter'''.
-Type '''java  -jar ./jchempaint-3.3-1210.jar''' and press enter.
+|-
-||Type ''''“cd space Desktop”''' and press enter.
+||Type '''java  -jar ./jchempaint-3.3-1210.jar''' and press '''Enter'''.
 '''JChemPaint''' window opens.
@@ Line 182: / Line 183: @@
 ||I will choose '''Alkali Earth Metals'''.
- '''Alkali Earth Metals''' list opens.
+'''Alkali Earth Metals''' list opens.
 |-
 ||Select the '''Calcium''' from the list.
@@ Line 216: / Line 217: @@
 |-
 ||Click on '''Save''' button the tool bar.
-|| Let's save the file now.
+|| Let us save the file now.
 Click on '''Save''' button on the tool bar.
 |-
 ||Point to the dialogue box.
-||'''Save''' dialogue box opens.
+||'''Save''' dialog box opens.
 |-
 ||Type the file name as '''Calcium-fluoride'''.
@@ Line 303: / Line 304: @@
 ||Right click on terminal '''Carbon''' atom.
- '''Atom Pop menu''' opens.
+'''Atom Pop menu''' opens.
 |-
 ||Point to the submenu.
 ||Scroll down to '''Pseudo Atoms'''.
-A submenu opens select '''R1'''.
+A submenu opens; select '''R1'''.
 |-
 ||
@@ Line 330: / Line 331: @@
 Go to '''R-groups''' menu and select '''Define as Substituent'''.
-||Click on '''Selection''' button, select the '''Substituent'''.
+||Click on '''Selection''' button; select the '''Substituent'''.
 Go to '''R-groups''' menu and select '''Define as Substituent'''.
@@ Line 339: / Line 340: @@
 || An input box opens.
-Here enter an '''R-group''' number as “1” and click '''OK''' button.
+Here, enter an '''R-group''' number as “1” and click '''OK''' button.
 The substituent will be numbered as '''R1'''.
@@ Line 346: / Line 347: @@
 Point to the substituent marked with asterisk(*)
-|| On the '''Root structure''' the substituent '''R1''' will be marked as asterisk(*)
+|| On the '''Root structure,''' the substituent '''R1''' will be marked as asterisk(*)
-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(*).
 |-
 ||Click on '''Selection''' button>> select '''Root Structure''' and  '''substituent(R1)'''.
-||Click on the '''Selection''' button,  select  the '''Root Structure''' and  '''substituent(R1)'''.
+||Click on the '''Selection''' button,  select  '''Root Structure''' and  '''substituent(R1)'''.
 |-
 ||Go to '''R-groups''' menu>>  select '''General Possible configurations(sdf)'''.
 || Go to '''R-groups''' menu,  select '''General Possible configurations(sdf)'''.
 |-
-||Point to the dialogue box.
+||Point to the dialog box.
-||'''Save''' dialogue box opens.
+||'''Save''' dialog box opens.
 |-
 ||Type the file name as '''r-group''' >>select the file location as '''Desktop'''.
@@ Line 379: / Line 380: @@
 ||Click on '''Desktop''' folder.
-Click '''Open''' then select the saved '''r-group''' file.
+Click '''Open'''; then select the saved '''r-group''' file.
 Click on “Open” button.
 |-
 ||Point to OK
-||A message pops up, click '''OK'''.
+||A message pops up; click '''OK'''.
 |-
 ||Move the cursor on the file.
@@ Line 409: / Line 410: @@
 * Draw a reaction
-* Set up R-Group query.
+* Set up '''R-Group query'''.
 |-
 ||'''Slide Number 7
@@ Line 417: / Line 418: @@
 * Explore various Periodic table trends and
 * Draw reactions of your choice.
 |-