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

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* Various Model types and how to  
 
* Various Model types and how to  
  
−
* Change the background color.
+
* Change background color.
 
|-
 
|-
 
||'''Slide Number 3'''
 
||'''Slide Number 3'''
Line 40: Line 40:
 
'''GChemPaint''' version 0.12.10.
 
'''GChemPaint''' version 0.12.10.
  
−
'''GChem3D''' version 0.12.10
+
'''GChem3D''' version 0.12.10
 
|-
 
|-
 
||'''Slide Number 4'''
 
||'''Slide Number 4'''
Line 47: Line 47:
 
||To follow this tutorial you should be familiar with '''GChemPaint''' .
 
||To follow this tutorial you should be familiar with '''GChemPaint''' .
  
−
If not, for relevant tutorials, please visit our website.
+
If not, for relevant tutorials, please visit our website.
 
|-
 
|-
 
||Switch to '''GChemPaint''' window
 
||Switch to '''GChemPaint''' window
Line 53: Line 53:
 
|-
 
|-
 
||Point to '''Templates''' tool drop down.
 
||Point to '''Templates''' tool drop down.
−
||Using '''Templates''' drop down I will load the structure of '''Adenosine'''.
+
||Using '''Templates''' drop down,
 +
 
 +
I will load the structure of '''Adenosine''' onto the '''Display area'''.
 
|-
 
|-
 
||Click on '''Save''' icon on the tool bar>>
 
||Click on '''Save''' icon on the tool bar>>
Line 64: Line 66:
 
||
 
||
 
||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.'''
Line 92: Line 94:
 
||Go to '''Synapatic Package Manager'''.
 
||Go to '''Synapatic Package Manager'''.
  
−
Type '''GChemPaint''' in the '''Quick filter box'''.
+
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'''.
 
||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
+
Install '''gcu-plugin''', '''libgcu-dbg''' and '''gcu-bin''' for complete installation of '''GChemPaint''' utilities.
−
 
+
−
''gcu-bin''
+
−
 
+
−
for complete installation of '''GChemPaint''' utilities.
+
  
 
I had already installed all the files.
 
I had already installed all the files.
Line 115: Line 108:
  
 
'''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'''.
 
It is a utility feature of '''GChemPaint'''.
Line 121: Line 114:
 
Structures  drawn in '''GChemPaint''' can be viewed in '''GChem3D'''
 
Structures  drawn in '''GChemPaint''' can be viewed in '''GChem3D'''
 
|-
 
|-
−
||Click on '''Dash Home''' type '''GChem3D''' in the search bar>>
+
||Click on '''Dash Home''' type '''gchem3d''' in the search bar>>
  
 
Click on '''Molecules viewer''' icon.
 
Click on '''Molecules viewer''' icon.
−
||To open '''GChem3D''' click on '''Dash Home''' type '''GChem3D''' in the search bar.
+
||To open '''GChem3D''' click on '''Dash Home'''.
−
 
+
−
Click on '''Molecules viewer''' icon that appears.
+
−
|-
+
−
||Press '''CTRL+ALT+T'''  keys simultaneously 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.
+
In the '''search bar''' that appears, type '''gchem3d'''.  
  
−
This will open '''GChem3D'''.
+
Click on '''Molecules viewer''' icon.  
 
|-
 
|-
 
||Point to '''GChem3d''' window.
 
||Point to '''GChem3d''' window.
Line 145: Line 129:
 
'''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''' dialogue box opens.  
+
'''Open''' dialog box opens.  
−
||To open a file, Select''' File''' select '''Open'''.
+
||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'''
 
||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.
+
I will select '''Adenosine.pdb''' on my Desktop.
  
−
Now click on ''' Open'''.
+
Now click on ''' Open''' button.
 
|-
 
|-
 
||Point to main window.
 
||Point to main window.
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|-
 
|-
 
||
 
||
−
||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.
+
Navigate to '''Save As Image'''
−
||Select '''File'''. 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.
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|-
 
|-
 
||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.
 
||Point to the '''File type''' drop down list.
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'''GChem3D''' supports various file formats.
 
'''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,
+
||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.
 
If it does not succeed, the default '''File type VRML''' will be used.
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||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
 
 
|-
 
|-
 
||
 
||
Line 223: Line 206:
 
||VRML is a text file format with '''.wrl''' extension.  
 
||VRML is a text file format with '''.wrl''' extension.  
  
−
3D polygon properties like vertices, edges, surface color can be specified  
+
3D polygon properties like ''''vertices', 'edges', 'surface color'''' can be specified.
  
 
'''VRML''' files are in plain text that compress as '''gzip'''.  
 
'''VRML''' files are in plain text that compress as '''gzip'''.  
  
−
3D modeling programs can save objects and scenes in '''VRML''' format.
+
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'''.
Line 236: Line 219:
 
Right click on the file '''Adenosine.wrl'''.
 
Right click on the file '''Adenosine.wrl'''.
  
−
Choose '''Open with Text Editor'''.
+
Choose option '''Open with Text Editor'''.
  
−
Text editor shows all the details about the structure
+
Text editor shows all the details about the structure.
 
|-
 
|-
 
||
 
||
−
||Next we move on to''' Page Setup'''.
+
||Now let's 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'''.
 
'''Page Setup''' properties are the same as in '''GChemPaint'''.
  
−
I had already discussed this in '''GChemPaint''' tutorials in this series
+
I had already discussed in the '''GChemPaint''' tutorials in this series
 +
|-
 +
||Point to 'Close' button.
 +
||I will close the window.
 
|-
 
|-
 
||
 
||
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|-
 
|-
 
||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
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||Point to '''Wireframe''' model
 
||Point to '''Wireframe''' model
 
||'''Wireframe''' model shows the ''skeletal'' structure.
 
||'''Wireframe''' model shows the ''skeletal'' structure.
 +
|-
 +
||Point to the structure.
 +
||Let's switch back to '''Balls and sticks'''.
 
|-
 
|-
 
||Point to the '''Background color'''
 
||Point to the '''Background color'''
 
||Now we move on to ''' Background color'''.
 
||Now we move on to ''' Background color'''.
  
−
Default background color is “black”.
+
Default background color is “black”.
 
|-
 
|-
−
||Select '''View''' menu and navigate to '''Background color'''.
+
||Select '''View''' menu,  navigate to '''Background color'''.
−
||Select '''View''' menu and 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.
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|-
 
|-
 
||Point to the Field.
 
||Point to the Field.
−
||Using '''Value''', we can change the '''RGB combination''' to get different shades of the color.
+
||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'''
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||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.
Line 333: Line 322:
 
||Click on '''Ok''' button.
 
||Click on '''Ok''' button.
  
−
Background color changes on the screen.<Pause>
+
Background color changes on the screen. <Pause>
 
|-
 
|-
 
||
 
||
Line 347: Line 336:
 
* File type formats
 
* File type formats
  
−
* Model types  
+
* Model types and
  
−
* Change background color.
+
* How to Change background color.
 
|-
 
|-
 
||'''Slide Number 9'''
 
||'''Slide Number 9'''
Line 356: Line 345:
 
||Here is an assignment  
 
||Here is an assignment  
  
−
1. Load a '''Saccharide''' from '''GChemPaint''' and save the file in '''.mdl'''
+
1. Load a '''Saccharide''' from the '''GChemPaint''' and save the file in '''.mdl''' format.
  
−
2. Open the structure of '''Saccharide''' in '''Molecules viewer'''.
+
2. Open the structure in '''Molecules viewer'''.
  
 
3. Save image in '''PNG''' and '''PDF''' file types.
 
3. Save image in '''PNG''' and '''PDF''' file types.

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

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