Difference between revisions of "GChemPaint/C3/Features-of-GChem3D/English"

From Script | Spoken-Tutorial
Jump to: navigation, search
(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…')
 
 
(4 intermediate revisions by one other user not shown)
Line 3: Line 3:
 
Author: '''Madhuri Ganapathi'''
 
Author: '''Madhuri Ganapathi'''
  
−
Key words: Menubar,  File types,  Model types,  Change Background color,  Video tutorial  
+
Key words: '''Menubar,  File types,  Model types,  Change Background color,  Video tutorial'''
−
 
+
  
 
<font size="2">
 
<font size="2">
Line 17: Line 16:
 
||Hello everyone.
 
||Hello everyone.
  
−
Welcome to this tutorial on '''Features of GChem3D '''.
+
Welcome to this tutorial on '''Features of GChem3D'''.
 
|-
 
|-
−
||Slide Number 2
+
||'''Slide Number 2'''
−
Learning Objectives
+
 
 +
'''Learning Objectives'''
 
||In this tutorial, we will learn about
 
||In this tutorial, we will learn about
−
Menu bar
+
 
−
File type formats
+
* Menu bar
−
Various Model types and how to  
+
 
−
Change the background color.
+
* File type formats
 +
 
 +
* Various Model types and how to  
 +
 
 +
* Change background color.
 
|-
 
|-
−
||Slide Number 3
+
||'''Slide Number 3'''
−
System Requirement
+
 
 +
'''System Requirement'''
 
||For this tutorial  I am using
 
||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
+
'''Ubuntu Linux''' OS version  12.04.
−
Pre-requisites
+
 
−
||To follow this tutorial you should be familiar with GChemPaint .
+
'''GChemPaint''' version 0.12.10.
−
If not, for relevant tutorials,  please visit our website.
+
 
 +
'''GChem3D''' version 0.12.10
 
|-
 
|-
−
||Switch to GChemPaint window
+
||'''Slide Number 4'''
−
||I have opened a new GChemPaint window.
+
 
 +
'''Pre-requisites'''
 +
||To follow this tutorial you should be familiar with '''GChemPaint''' .
  
 +
If not, for relevant tutorials, please visit our website.
 
|-
 
|-
−
||Point to Templates tool drop down.
+
||Switch to '''GChemPaint''' window
−
||Using Templates drop down I will load the structure of Adenosine.
+
||I have opened a new '''GChemPaint''' window.
 
|-
 
|-
 +
||Point to '''Templates''' tool drop down.
 +
||Using '''Templates''' drop down,
  
−
||Click on Save icon on the tool bar>>
+
I will load the structure of '''Adenosine''' onto the '''Display area'''.
−
Save as dialog box opens.
+
|-
−
||To save the file click Save icon on the tool bar.
+
||Click on '''Save''' icon on the tool bar>>
−
Save as dialog box opens.
+
 
 +
'''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  
−
To view the file in GChem3D, it has to saved in  
+
file formats like,
−
file formats like .mol, .mdl and .pdb.
+
 
 +
'''.mol, .mdl''' and '''.pdb.'''
 
|-
 
|-
−
||Type file name as Adenosine.pdb
+
||Type file name as '''Adenosine.pdb'''
−
Click  Desktop to save the file on Desktop>>Click on Save  
+
 
 +
Click  '''Desktop''' to save the file on '''Desktop'''>>Click on Save  
 
||Type the file name as Adenosine.pdb
 
||Type the file name as Adenosine.pdb
−
Click Desktop to save the file on Desktop.
 
−
Click on Save button.
 
  
−
|-
+
Click '''Desktop''' to save the file on''' Desktop'''.
  
−
||Point to the Close button.
+
Click on '''Save''' button.
−
||I will close the GChemPaint window.
+
|-
 +
||Point to the '''Close''' button.
 +
||I will close the '''GChemPaint''' window.
 
|-
 
|-
 
||
 
||
−
||Let's now learn about GChem3d application.
+
||Let's now learn about '''GChem3D''' application.
 
|-
 
|-
−
||Slide Number 5
+
||'''Slide Number 5'''
−
Installation
+
 
−
||GChem3D can be installed as a utility software of GChemPaint using Synaptic Package Manager.
+
'''Installation'''
 +
||'''GChem3D''' can be installed as a utility software of '''GChemPaint''',
  
 +
using ''' Synaptic Package Manager'''.
 
|-
 
|-
−
||Go to Synapatic Package Manager.
+
||Go to '''Synapatic Package Manager'''.
−
Type GChemPaint in the Quick filter box.
+
 
−
Point to gcu-bin
+
In the '''Quick filter box''' type '''gchempaint'''.
−
gcu-plugin and
+
 
−
libgcu-dbg
+
Install '''gcu-plugin''', '''libgcu-dbg''' and '''gcu-bin'''
−
||Go to Synaptic Package Manager.
+
||Go to '''Synaptic Package Manager'''.
−
Type GChemPaint in the Quick filter box.
+
 
−
Install gcu-plugin
+
In the '''Quick filter box''', type '''gchempaint'''.
−
libgcu-dbg and
+
 
−
gcu-bin
+
Install '''gcu-plugin''', '''libgcu-dbg''' and '''gcu-bin''' for complete installation of '''GChemPaint''' utilities.
  
−
for complete installation of GChemPaint utilities.
 
 
I had already installed all the files.
 
I had already installed all the files.
 
|-
 
|-
−
||Slide Number 6
+
||'''Slide Number 6'''
−
About GChem3d
+
 
−
||
+
'''About GChem3d'''
−
GChem3d is a 3 dimensional molecular structures visualizer.
+
||'''GChem3d''' is a 3 dimensional molecular structure visualizer.
−
It is a utility feature of GChemPaint.
+
 
−
Structures  drawn in GChemPaint can be viewed in GChem3D
+
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.
+
||Click on '''Dash Home''' type '''gchem3d''' in the search bar>>
−
||To open GChem3d click on Dash Home type GChem3D in the search bar.
+
 
−
Click on Molecules viewer icon that appears.
+
Click on '''Molecules viewer''' icon.
−
|-
+
||To open '''GChem3D''' click on '''Dash Home'''.
−
||Press CTRL+ALT+ T  keys simultanueously to open the terminal.
+
 
−
Type “gchem3d” and press enter.
+
In the '''search bar''' that appears, type '''gchem3d'''.  
−
||Alternatively you can also open GChem3D using Terminal.
+
 
−
Press CTRL+ALT+ T  keys simultaneously to open the terminal.
+
Click on '''Molecules viewer''' icon.  
−
Type “gchem3d” and press Enter.
+
−
This will open GChem3D.
+
 
|-
 
|-
−
||Point to GChem3d window.
+
||Point to '''GChem3d''' window.
  
−
Point to Menubar
+
Point to '''Menubar'''
 
||
 
||
−
GChem3d Viewer window contains  Menubar and Display area.
+
'''GChem3d Viewer''' window contains  '''Menubar''' and '''Display area'''.
−
Menubar contains all the commands you need to work in GChem3d.
+
 
 +
'''Menubar''' contains all the commands you need to work with '''GChem3D'''.
 
|-
 
|-
 
||Point to Display area
 
||Point to Display area
−
||Display area shows the contents of an opened file.
+
||'''Display area''' shows the contents of an opened file.
 
|-
 
|-
−
||Select File click on Open.
+
||Select''' File'''.  Click on '''Open'''.
−
Open file dialogue box opens.  
+
 
−
||To open a file, Select File select  Open.
+
'''Open''' dialog box opens.  
−
Open dialogue box opens.  
+
||To open a file, Select ''' File''' click on '''Open'''.
 +
 
 +
'''Open''' dialog box opens.  
 
|-
 
|-
−
||
+
||Select the file that you want to open>>click '''Open'''
−
Select the file that you want to open>>click Open
+
 
||Select the file that you want to open.
 
||Select the file that you want to open.
−
I will select Adenosine.pdb from my Desktop folder.
+
 
−
Now click on Open.
+
I will select '''Adenosine.pdb''' on my Desktop.
 +
 
 +
Now click on ''' Open''' button.
 
|-
 
|-
 
||Point to main window.
 
||Point to main window.
−
||File is displayed on the Display area.  
+
||File is displayed on the '''Display area'''.  
 
|-
 
|-
 
||
 
||
−
||
+
||Let's learn to save the view as an image.
−
Let's learn to Save the view as an Image.
+
 
|-
 
|-
−
||Select File navigate to Save As Image
+
||Click on '''File'''.
−
Save as image dialogue box opens.
+
 
−
||Select File. Navigate to Save As Image
+
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''' dialog box opens.
 
|-
 
|-
 
||Point to the Width  and Height.
 
||Point to the Width  and Height.
−
||Notice Width and Height parameters at the bottom.
+
||Notice ''' Width''' and '''Height''' parameters at the bottom.
  
−
Default image size has Width 300 pixels and Height 300 pixels.
+
Default image size has '''Width''' ''300 pixels'' and '''Height''' ''300 pixels''.
 
|-
 
|-
 
||Point to the scrollers.
 
||Point to the scrollers.
−
||You can increase or decrease these values using the scrollers.
+
||You can increase or decrease the values using the scrollers.
 
|-
 
|-
−
||
+
||Point to the '''File type''' drop down list.
 +
||Now to '''File type''' option.
  
−
Point to the File type drop down list.
+
'''GChem3D''' supports various file formats.
−
||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.
+
File types like '''VRML, PDF, PNG''' and others are available in the drop-down list.
 
|-
 
|-
−
||Point to VRML File type.
+
||Point to '''VRML File''' type.
−
||If no file type is specified, GChem3d tries to determine file type from the file name.
+
||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.
+
 
 +
If it does not succeed, the default '''File type VRML''' will be used.
 
|-
 
|-
−
||
+
||Select the option VRML document.
−
||
+
||Let's save the structure in '''VRML''' file format.  
−
Let's save the structure in VRML file format.
+
−
Select the option VRML document.
+
  
 +
Select the option '''VRML document'''.
 
|-
 
|-
−
||Type the file name as Adenosine.
+
||Type the file name as '''Adenosine'''.
−
||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'''  to save the file on '''Desktop'''.
−
||Click on Desktop folder to save the file on Desktop.
+
||Click on '''Desktop'''  to save the file on '''Desktop'''.
 
|-
 
|-
 +
||Click on '''Save''' button.
 +
||Click on '''Save''' button.
  
−
||Click on Save button.
 
−
||
 
−
Click on Save button.
 
−
File saves with .wrl extension
 
 
|-
 
|-
 
||
 
||
−
||
+
||Now we will learn what exactly is '''VRML File type'''.
−
Now we will learn what exactly is VRML File type.
+
 
|-
 
|-
−
||Slide Number 7
+
||'''Slide Number 7'''
−
VMRL File format
+
 
−
||VRML is a text file format with .wrl extension.  
+
'''VMRL File format'''
−
3D polygon properties like vertices, edges, surface color can be specified  
+
||VRML is a text file format with '''.wrl''' extension.  
−
VRML files are in plain text that compress as gzip.  
+
 
−
3D modeling programs can save objects and scenes in VRML format.
+
3D polygon properties like ''''vertices', 'edges', 'surface color'''' can be specified.
 +
 
 +
'''VRML''' files are in plain text that compress as '''gzip'''.  
 +
 
 +
3D modeling programs save objects and scenes in it.
 
|-
 
|-
−
||Right click on the file Open with Text Editor.
+
||Right click on the file '''Open with Text Editor'''.
  
 
Scroll down the editor.
 
Scroll down the editor.
 
||Let's open the saved file.
 
||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
+
Right click on the file '''Adenosine.wrl'''.
 +
 
 +
Choose option '''Open with Text Editor'''.
 +
 
 +
Text editor shows all the details about the structure.
 
|-
 
|-
 
||
 
||
−
||
+
||Now let's move on to ''' Page Setup'''.
−
Next we move on to Page Setup.
+
 
|-
 
|-
−
||Point to Page Setup menu
+
||Point to '''Page Setup''' menu
−
||GChem3d uses a 300 dpi resolution while printing.
+
||'''GChem3d''' uses '''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
+
'''Page Setup''' properties are the same as in '''GChemPaint'''.
 +
 
 +
I had already discussed in the '''GChemPaint''' tutorials in this series
 
|-
 
|-
−
||
+
||Point to 'Close' button.
−
||
+
||I will close the window.
−
Now let's move on to View menu.
+
 
|-
 
|-
−
||Select View menu.
 
 
||
 
||
−
Select View menu.
+
||Now let's move on to '''View''' menu.
−
GChem3D displays a molecule using four model types:
+
|-
−
Ball and sticks
+
||Select '''View''' menu.
−
Space filling
+
||Select '''View''' menu.
−
Cylinders  and
+
−
Wireframe.  
+
  
 +
'''GChem3D''' displays a molecule using four model types:
 +
 +
* Balls and sticks
 +
 +
* Space filling
 +
 +
* Cylinders  and
 +
 +
* Wireframe.
 
|-
 
|-
−
||Point to Ball and sticks model.
+
||Point to '''Balls and sticks''' model.
−
||Ball and sticks is the default model.
+
||'''Balls and sticks''' is the default model.
 +
 
 
Multiple bond and correct bond positions can be viewed using this model.
 
Multiple bond and correct bond positions can be viewed using this model.
 
|-
 
|-
−
||Point to Space filling model
+
||Point to '''Space filling''' model
−
||I will click on Space Filling and you can see the difference.
+
||I will click on '''Space Filling''' and you can see the difference.
−
Space filling model shows the molecules in compact form.
+
 
 +
'''Space Filling''' model shows the molecules in compact form.
 
|-
 
|-
−
||Point to Cylinders model
+
||Point to '''Cylinders''' model
−
||Cylinders model shows the structure in the form of cylindrical pipes.
+
||'''Cylinders''' model shows the structure in the form of ''cylindrical pipes''.
 
|-
 
|-
−
||Point to Wireframe model
+
||Point to '''Wireframe''' model
−
||Wireframe model shows the skeletal structure.
+
||'''Wireframe''' model shows the ''skeletal'' structure.
 
|-
 
|-
−
||Point to the background color
+
||Point to the structure.
−
||Now we move on to Background color.
+
||Let's switch back to '''Balls and sticks'''.
−
Default background  color is “ black”.
+
 
|-
 
|-
−
||Select View menu and navigate to Background color.
+
||Point to the '''Background color'''
−
||Select View menu and navigate to Background color.
+
||Now we move on to ''' Background color'''.
 +
 
 +
Default background color is “black”.
 +
|-
 +
||Select '''View''' menu,  navigate to '''Background color'''.
 +
||Select '''View''' menu,  navigate to '''Background color'''.
 
|-
 
|-
 
||A submenu opens.
 
||A submenu opens.
 
||A submenu opens.
 
||A submenu opens.
 
|-
 
|-
−
||Click on Custom color at the end.
+
||Select '''Custom color''' at the end.
  
 
Point to window
 
Point to window
−
||Click on Custom color at the end of the submenu.
+
||Select '''Custom color''' at the end of submenu.
−
Background color window opens.
+
 
 +
'''Background color''' window opens.
 
|-
 
|-
 
||Point to all the Fields.
 
||Point to all the Fields.
−
||
+
||This window has various fields to choose the color we want.
−
This window has various fields to choose the colour we want.
+
 
|-
 
|-
 
||Point to the Field.
 
||Point to the Field.
−
||Using Hue, we can change the background color.
+
||Using '''Hue''', we can change the background color.
 
|-
 
|-
 
||Click on the scroller.
 
||Click on the scroller.
−
Point to the color circle.
+
 
 +
Point to the ''color circle''.
 
||Click on the scroller.
 
||Click on the scroller.
−
Notice the change in value and movement of the color circle.
+
 
 +
Notice the change in value and movement of the ''color circle''.
 
|-
 
|-
 
||Point to the Field.
 
||Point to the Field.
−
||Using Saturation, we can change the concentration of the color.
+
||Using '''Saturation''', we can change the concentration of the color.
 
|-
 
|-
 
||Point to the Field.
 
||Point to the Field.
−
||Using Value, we can change the RGB combination to get different shades of the colour.
+
||Using '''Value''', we can change the '''RGB combination''' to get different shades of the same color.
 
|-
 
|-
−
||Point to preview box and then to eyedropper
+
||Point to '''Preview box''' and then to '''eyedropper'''
−
||Here is the preview box with an eyedropper icon next to it.
+
||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 on the color ring
−
Click on eyedropper icon.
+
 
−
||
+
||Click on the '''eyedropper''' icon.
 +
 
 
Click anywhere on the color ring to choose the preferred color.
 
Click anywhere on the color ring to choose the preferred color.
 
|-
 
|-
−
||Click on Ok button.
+
||Click on '''Ok''' button.
 +
 
 
Point to changed background color
 
Point to changed background color
−
||Click on Ok button.
+
||Click on '''Ok''' button.
−
Background color changes on the screen.<Pause>
+
 
 +
Background color changes on the screen. <Pause>
 
|-
 
|-
 
||
 
||
−
||
+
||Let's summarize what we have learnt.
−
Let's summarize what we have learnt.
+
 
|-
 
|-
−
||Slide Number 8
+
||'''Slide Number 8'''
−
Summary
+
 
 +
'''Summary'''
 
||In this tutorial we have learnt about,
 
||In this tutorial we have learnt about,
−
Different Menus
+
 
−
File type formats
+
* Different Menus
−
Model types  
+
 
−
Change background color.
+
* File type formats
 +
 
 +
* Model types and
 +
 
 +
* How to Change background color.
 
|-
 
|-
−
||Slide Number 9
+
||'''Slide Number 9'''
−
Assignment
+
 
 +
'''Assignment'''
 
||Here is an 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.
+
1. Load a '''Saccharide''' from the '''GChemPaint''' and save the file in '''.mdl''' format.
−
3. Save image in PNG and PDF file types.
+
 
 +
2. Open the structure in '''Molecules viewer'''.
 +
 
 +
3. Save image in '''PNG''' and '''PDF''' file types.
 +
 
 
4. Try various background colors.
 
4. Try various background colors.
 
|-
 
|-
−
||Slide Number 10
+
||'''Slide Number 10'''
−
Acknowledgement  
+
 
 +
'''Acknowledgement'''
 
||Watch the video available at this URL.
 
||Watch the video available at this URL.
−
http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial
+
 
 +
'''http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial'''
 +
 
 
It summarizes the Spoken Tutorial project
 
It summarizes the Spoken Tutorial project
 +
 
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  
 
|-
 
|-
−
||Slide Number 11
+
||'''Slide Number 11'''
 
||The Spoken Tutorial Project Team:  
 
||The Spoken Tutorial Project Team:  
 +
 
Conducts workshops using spoken tutorials
 
Conducts workshops using spoken tutorials
 +
 
Gives certificates to those who pass an on-line test  
 
Gives certificates to those who pass an on-line test  
 +
 
For more details, please write to  
 
For more details, please write to  
−
contact@spoken-tutorial.org
 
  
 +
'''contact@spoken-tutorial.org'''
 
|-
 
|-
−
||
+
||'''Slide number 12'''
−
Slide number 12
+
 
||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  
 +
 
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
−
More information on this Mission is available at this link http://spoken-tutorial.org/NMEICT-Intro]
+
 
 +
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.  
 
|-
 
|-
−
}
 

Latest revision as of 09:46, 3 April 2014

Title of the tutorial: Features of GChem3D

Author: Madhuri Ganapathi

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

Visual Cue Narration

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 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 onto the Display area.

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.

In the Quick filter box type gchempaint.

Install gcu-plugin, libgcu-dbg and gcu-bin

Go to Synaptic Package Manager.

In the Quick filter box, type gchempaint.

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 structure 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.

In the search bar that appears, type gchem3d.

Click on Molecules viewer icon.

Point to GChem3d window.

Point to Menubar

GChem3d Viewer window contains Menubar and Display area.

Menubar contains all the commands you need to work with GChem3D.

Point to Display area Display area shows the contents of an opened file.
Select File. Click on Open.

Open dialog box opens.

To open a file, Select File click on Open.

Open dialog 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 on my Desktop.

Now click on Open button.

Point to main window. File is displayed on the Display area.
Let's learn to save the view as an image.
Click on File.

Navigate to Save As Image

Save as image dialog box opens.

Click on File. Navigate to Save As Image.

Save as image dialog 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 the 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.

Select the option VRML document. 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 to save the file on Desktop. Click on Desktop to save the file on Desktop.
Click on Save button. Click on Save button.
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 save objects and scenes in it.

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 option Open with Text Editor.

Text editor shows all the details about the structure.

Now let's move on to Page Setup.
Point to Page Setup menu GChem3d uses 300 dpi resolution while printing.

Page Setup properties are the same as in GChemPaint.

I had already discussed in the GChemPaint tutorials in this series

Point to 'Close' button. I will close the window.
Now let's move on to View menu.
Select View menu. Select View menu.

GChem3D displays a molecule using four model types:

  • Balls and sticks
  • Space filling
  • Cylinders and
  • Wireframe.
Point to Balls and sticks model. Balls 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 structure. Let's switch back to Balls and sticks.
Point to the Background color Now we move on to Background color.

Default background color is “black”.

Select View menu, navigate to Background color. Select View menu, navigate to Background color.
A submenu opens. A submenu opens.
Select Custom color at the end.

Point to window

Select Custom color at the end of submenu.

Background color window opens.

Point to all the Fields. This window has various fields to choose the color 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 same color.
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 the 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 and
  • How to Change background color.
Slide Number 9

Assignment

Here is an assignment

1. Load a Saccharide from the GChemPaint and save the file in .mdl format.

2. Open the structure 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.

Contributors and Content Editors

Madhurig, Nancyvarkey

Retrieved from "https://script.spoken-tutorial.org/index.php?title=GChemPaint/C3/Features-of-GChem3D/English&oldid=9631"