Difference between revisions of "GChemPaint/C3/Features-of-GChem3D/English"
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In the '''Quick filter box''' type '''gchempaint'''. | 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'''. | ||
| − | In the '''Quick filter box''' type '''gchempaint'''. | + | In the '''Quick filter box''', type '''gchempaint'''. |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | 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. | I had already installed all the files. | ||
| Line 127: | Line 117: | ||
Click on '''Molecules viewer''' icon. | Click on '''Molecules viewer''' icon. | ||
| − | ||To open '''GChem3D''' click on '''Dash Home''' | + | ||To open '''GChem3D''' click on '''Dash Home'''. |
| + | |||
| + | In the '''search bar''' that appears, type '''gchem3d'''. | ||
Click on '''Molecules viewer''' icon. | Click on '''Molecules viewer''' icon. | ||
| Line 142: | Line 134: | ||
||'''Display area''' shows the contents of an opened file. | ||'''Display area''' shows the contents of an opened file. | ||
|- | |- | ||
| − | ||Select''' File''' | + | ||Select''' File'''. Click on '''Open'''. |
| − | '''Open''' | + | '''Open''' dialog box opens. |
||To open a file, Select ''' File''' click on '''Open'''. | ||To open a file, Select ''' File''' click on '''Open'''. | ||
| − | '''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''' | ||
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|- | |- | ||
|| | || | ||
| − | ||Let's learn to | + | ||Let's learn to save the view as an image. |
|- | |- | ||
||Click on '''File'''. | ||Click on '''File'''. | ||
| Line 166: | Line 158: | ||
Navigate to '''Save As Image''' | Navigate to '''Save As Image''' | ||
| − | '''Save as image''' | + | '''Save as image''' dialog box opens. |
||Click on '''File'''. Navigate to '''Save As Image'''. | ||Click on '''File'''. Navigate to '''Save As Image'''. | ||
| − | '''Save as image''' | + | '''Save as image''' dialog box opens. |
|- | |- | ||
||Point to the Width and Height. | ||Point to the Width and Height. | ||
| Line 187: | Line 179: | ||
|- | |- | ||
||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. | ||
| Line 216: | 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 save objects and scenes | + | 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'''. | ||
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
|
| 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:
|
| 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,
|
| 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 |
| This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining. |
