GChemPaint/C3/Features-of-GChem3D/English - Revision history

Nancyvarkey at 04:16, 3 April 2014

2014-04-03T04:16:37Z

Madhurig at 07:15, 1 April 2014

2014-04-01T07:15:24Z

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Madhurig at 07:49, 26 March 2014

2014-03-26T07:49:42Z

Madhurig at 07:46, 26 March 2014

2014-03-26T07:46:41Z

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Madhurig at 07:18, 26 March 2014

2014-03-26T07:18:21Z

Madhurig: Created page with 'Title of the tutorial: '''Features of GChem3D''' Author: '''Madhuri Ganapathi''' Key words: Menubar, File types, Model types, Change Background color, Video tutorial
2014-03-26T07:16:04Z

Created page with 'Title of the tutorial: '''Features of GChem3D''' Author: '''Madhuri Ganapathi''' Key words: Menubar, File types, Model types, Change Background color, Video tutorial <fo…'

New page
Title of the tutorial: '''Features of GChem3D'''

Author: '''Madhuri Ganapathi'''

Key words: Menubar, File types, Model types, Change Background color, Video tutorial

<font size="2">
{|border=1
!'''Visual Cue'''
!'''Narration'''
</font>
|-
||'''Slide Number 1'''

'''Title Slide'''
||Hello everyone.

Welcome to this tutorial on '''Features of GChem3D '''.
|-
||Slide Number 2
Learning Objectives
||In this tutorial, we will learn about
Menu bar
File type formats
Various Model types and how to
Change the background color.
|-
||Slide Number 3
System Requirement
||For this tutorial I am using
Ubuntu Linux OS version 12.04.
GChemPaint version 0.12.10.
GChem3D version 0.12.10
|-
||

Slide Number 4
Pre-requisites
||To follow this tutorial you should be familiar with GChemPaint .
If not, for relevant tutorials, please visit our website.
|-
||Switch to GChemPaint window
||I have opened a new GChemPaint window.

|-
||Point to Templates tool drop down.
||Using Templates drop down I will load the structure of Adenosine.
|-

||Click on Save icon on the tool bar>>
Save as dialog box opens.
||To save the file click Save icon on the tool bar.
Save as dialog box opens.

|-
||
||
To view the file in GChem3D, it has to saved in
file formats like .mol, .mdl and .pdb.
|-
||Type file name as Adenosine.pdb
Click Desktop to save the file on Desktop>>Click on Save
||Type the file name as Adenosine.pdb
Click Desktop to save the file on Desktop.
Click on Save button.

|-

||Point to the Close button.
||I will close the GChemPaint window.
|-
||
||Let's now learn about GChem3d application.
|-
||Slide Number 5
Installation
||GChem3D can be installed as a utility software of GChemPaint using Synaptic Package Manager.

|-
||Go to Synapatic Package Manager.
Type GChemPaint in the Quick filter box.
Point to gcu-bin
gcu-plugin and
libgcu-dbg
||Go to Synaptic Package Manager.
Type GChemPaint in the Quick filter box.
Install gcu-plugin
libgcu-dbg and
gcu-bin

for complete installation of GChemPaint utilities.
I had already installed all the files.
|-
||Slide Number 6
About GChem3d
||
GChem3d is a 3 dimensional molecular structures visualizer.
It is a utility feature of GChemPaint.
Structures drawn in GChemPaint can be viewed in GChem3D
|-
||Click on Dash Home type GChem3D in the search bar>>Click on Molecules viewer icon.
||To open GChem3d click on Dash Home type GChem3D in the search bar.
Click on Molecules viewer icon that appears.
|-
||Press CTRL+ALT+ T keys simultanueously to open the terminal.
Type “gchem3d” and press enter.
||Alternatively you can also open GChem3D using Terminal.
Press CTRL+ALT+ T keys simultaneously to open the terminal.
Type “gchem3d” and press Enter.
This will open GChem3D.
|-
||Point to GChem3d window.

Point to Menubar
||
GChem3d Viewer window contains Menubar and Display area.
Menubar contains all the commands you need to work in GChem3d.
|-
||Point to Display area
||Display area shows the contents of an opened file.
|-
||Select File click on Open.
Open file dialogue box opens.
||To open a file, Select File select Open.
Open dialogue box opens.
|-
||
Select the file that you want to open>>click Open
||Select the file that you want to open.
I will select Adenosine.pdb from my Desktop folder.
Now click on Open.
|-
||Point to main window.
||File is displayed on the Display area.
|-
||
||
Let's learn to Save the view as an Image.
|-
||Select File navigate to Save As Image
Save as image dialogue box opens.
||Select File. Navigate to Save As Image
Save as image dialogue box opens.
|-
||Point to the Width and Height.
||Notice Width and Height parameters at the bottom.

Default image size has Width 300 pixels and Height 300 pixels.
|-
||Point to the scrollers.
||You can increase or decrease these values using the scrollers.
|-
||

Point to the File type drop down list.
||Now to File type option.
GChem3D supports various file formats.

File types like VRML, PDF, PNG and others are available in the drop-down list.
|-
||Point to VRML File type.
||If no file type is specified, GChem3d tries to determine file type from the file name.
If it does not succeed, the default File type VRML will be used.
|-
||
||
Let's save the structure in VRML file format.
Select the option VRML document.

|-
||Type the file name as Adenosine.
||Type the file name as Adenosine
|-
||Click on Desktop folder to save the file on Desktop.
||Click on Desktop folder to save the file on Desktop.
|-

||Click on Save button.
||
Click on Save button.
File saves with .wrl extension
|-
||
||
Now we will learn what exactly is VRML File type.
|-
||Slide Number 7
VMRL File format
||VRML is a text file format with .wrl extension.
3D polygon properties like vertices, edges, surface color can be specified
VRML files are in plain text that compress as gzip.
3D modeling programs can save objects and scenes in VRML format.
|-
||Right click on the file Open with Text Editor.

Scroll down the editor.
||Let's open the saved file.
Right click on the file ''Adenosine.wrl''.
Choose Open with Text Editor.

Text editor shows all the details about the structure
|-
||
||
Next we move on to Page Setup.
|-
||Point to Page Setup menu
||GChem3d uses a 300 dpi resolution while printing.
Page Setup properties are the same as in GChemPaint.
I had already discussed this in GChemPaint tutorials in this series
|-
||
||
Now let's move on to View menu.
|-
||Select View menu.
||
Select View menu.
GChem3D displays a molecule using four model types:
Ball and sticks
Space filling
Cylinders and
Wireframe.

|-
||Point to Ball and sticks model.
||Ball and sticks is the default model.
Multiple bond and correct bond positions can be viewed using this model.
|-
||Point to Space filling model
||I will click on Space Filling and you can see the difference.
Space filling model shows the molecules in compact form.
|-
||Point to Cylinders model
||Cylinders model shows the structure in the form of cylindrical pipes.
|-
||Point to Wireframe model
||Wireframe model shows the skeletal structure.
|-
||Point to the background color
||Now we move on to Background color.
Default background color is “ black”.
|-
||Select View menu and navigate to Background color.
||Select View menu and navigate to Background color.
|-
||A submenu opens.
||A submenu opens.
|-
||Click on Custom color at the end.

Point to window
||Click on Custom color at the end of the submenu.
Background color window opens.
|-
||Point to all the Fields.
||
This window has various fields to choose the colour we want.
|-
||Point to the Field.
||Using Hue, we can change the background color.
|-
||Click on the scroller.
Point to the color circle.
||Click on the scroller.
Notice the change in value and movement of the color circle.
|-
||Point to the Field.
||Using Saturation, we can change the concentration of the color.
|-
||Point to the Field.
||Using Value, we can change the RGB combination to get different shades of the colour.
|-
||Point to preview box and then to eyedropper
||Here is the preview box with an eyedropper icon next to it.
|-
||Click on eyedropper icon >> click on the color ring
Click on eyedropper icon.
||
Click anywhere on the color ring to choose the preferred color.
|-
||Click on Ok button.
Point to changed background color
||Click on Ok button.
Background color changes on the screen.<Pause>
|-
||
||
Let's summarize what we have learnt.
|-
||Slide Number 8
Summary
||In this tutorial we have learnt about,
Different Menus
File type formats
Model types
Change background color.
|-
||Slide Number 9
Assignment
||Here is an assignment
1. Load a Saccharide from GChemPaint and save the file in .mdl
2. Open the structure of Saccharide in Molecules viewer.
3. Save image in PNG and PDF file types.
4. Try various background colors.
|-
||Slide Number 10
Acknowledgement
||Watch the video available at this URL.
http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial
It summarizes the Spoken Tutorial project
If you do not have good bandwidth, you can download and watch it
|-
||Slide Number 11
||The Spoken Tutorial Project Team:
Conducts workshops using spoken tutorials
Gives certificates to those who pass an on-line test
For more details, please write to
contact@spoken-tutorial.org

|-
||
Slide number 12
||Spoken Tutorial Project is a part of the Talk to a Teacher project
It is supported by the National Mission on Education through ICT, 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 96: / Line 96: @@
 In the '''Quick filter box''' type '''gchempaint'''.
-Install ''gcu-plugin''
+Install '''gcu-plugin''', '''libgcu-dbg''' and '''gcu-bin'''
-−
 ''libgcu-dbg'' and
-−
 ''gcu-bin''
 ||Go to '''Synaptic Package Manager'''.
-In the '''Quick filter box''' type '''gchempaint'''.
+In the '''Quick filter box''', type '''gchempaint'''.
-−
-Install ''gcu-plugin''
-−
-''libgcu-dbg'' and
-−
-''gcu-bin''
-for complete installation of '''GChemPaint''' utilities.
+Install '''gcu-plugin''', '''libgcu-dbg''' and '''gcu-bin''' for complete installation of '''GChemPaint''' utilities.
 I had already installed all the files.
@@ Line 127: / Line 117: @@
 Click on '''Molecules viewer''' icon.
-||To open '''GChem3D''' click on '''Dash Home''' in the search bar that appears type '''gchem3d'''.
+||To open '''GChem3D''' click on '''Dash Home'''.
 Click on '''Molecules viewer''' icon.
@@ Line 142: / Line 134: @@
 ||'''Display area''' shows the contents of an opened file.
 |-
-||Select''' File''' click on '''Open'''.
+||Select''' File'''.  Click on '''Open'''.
-'''Open''' dialogue box opens.
+'''Open''' dialog box opens.
 ||To open a file, Select ''' File''' click on '''Open'''.
-'''Open''' dialogue box opens.
+'''Open''' dialog box opens.
 |-
 ||Select the file that you want to open>>click '''Open'''
@@ Line 160: / Line 152: @@
 |-
 ||
-||Let's learn to '''Save the view as an Image'''.
+||Let's learn to save the view as an image.
 |-
 ||Click on '''File'''.
@@ Line 166: / Line 158: @@
 Navigate to '''Save As Image'''
-'''Save as image''' dialogue box opens.
+'''Save as image''' dialog box opens.
 ||Click on '''File'''. Navigate to '''Save As Image'''.
-'''Save as image''' dialogue box opens.
+'''Save as image''' dialog box opens.
 |-
 ||Point to the Width  and Height.
@@ Line 187: / Line 179: @@
 |-
 ||Point to '''VRML File''' type.
-||If no file type is specified,
+||If no file type is specified, '''GChem3d''' tries to determine file type from the file name.
-−
 '''GChem3d''' tries to determine file type from the file name.
 If it does not succeed, the default '''File type VRML''' will be used.
@@ Line 216: / Line 206: @@
 ||VRML is a text file format with '''.wrl''' extension.
-D polygon properties like 'vertices', 'edges', 'surface color' can be specified.
+D polygon properties like ''''vertices', 'edges', 'surface color'''' can be specified.
 '''VRML''' files are in plain text that compress as '''gzip'''.
-D modeling programs save objects and scenes in '''VRML''' in it.
+D modeling programs save objects and scenes in it.
 |-
 ||Right click on the file '''Open with Text Editor'''.

@@ Line 4: / Line 4: @@
 Key words: '''Menubar,  File types,  Model types,  Change Background color,  Video tutorial'''
 <font size="2">
@@ Line 52: / Line 51: @@
 ||Switch to '''GChemPaint''' window
 ||I have opened a new '''GChemPaint''' window.
 |-
 ||Point to '''Templates''' tool drop down.
@@ Line 347: / Line 345: @@
 * Different Menus
-*File type formats
+* File type formats
-*Model types
+* Model types
-*Change background color.
+* Change background color.
 |-
 ||'''Slide Number 9'''

@@ Line 322: / Line 322: @@
 |-
 ||
-Slide number 12
+'''Slide number 12'''
 ||Spoken Tutorial Project is a part of the Talk to a Teacher project
 It is supported by the National Mission on Education through ICT, 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.
+||This is '''Madhuri Ganapathi''' from IIT '''Bombay signing''' off. Thank you for joining.
 |-