View source for ORCA---Computational-Chemistry/C2/Create-XYZ-File-using-Open-Babel/English

'''Title of the script''': Create XYZ File using Open Babel

'''Authors: '''Madhuri Ganapathi, Raj Singh, Snehalatha Kaliappan.

'''Keywords:''' ORCA, Open Babel, Jmol, XYZ file, mol file, SMILES string, orca input file, video tutorial.

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

'''Title slide'''
|| Welcome to this spoken tutorial on '''Create XYZ File using Open Babel'''.
|- 
|| '''Slide Number 2 '''

'''Learning Objectives'''
|| In this tutorial, we will learn to,
* Load water molecule in '''Jmol'''
* Save the file in mol format
* Create SMILES string
* Create XYZ file format using''' Open Babel'''.
|-
|| '''Slide Number 3'''

'''System Requirements'''
|| Here I am using,
* '''Ubuntu Linux '''OS version 22.04
* '''Jmol''' version 16.2.35
* '''Java''' version 11.0.25
* '''Gedit''' text editor version 41.0

A working internet connection.
|-
|| '''Slide Number 4'''

'''Pre-requisites'''

'''https://spoken-tutorial.org'''
|| To follow this tutorial, learners should be familiar with the''' Jmol''' interface.

Please watch the Jmol tutorials available on this website.
|-
|| Point to the interface.
|| I have opened the '''Jmol''' interface.
|-
|| Click on File and select '''Get MOL''' option.

In the text box that appears type water and click '''OK''' button.
|| Let us load the water molecule on the Jmol panel.

Click on '''File '''and select '''Get MOL '''option.

In the text box that appears, type water and click '''OK '''button.
|-
|| Point to the water molecule.

Click on the Open model kit icon on the tool bar.

From the options click on minimize.
|| A water molecule appears on the panel.

Click on the '''model kit''' icon.

From the options select '''minimize''' to minimize the structure.
|-
|| Click on Open the model kit.

Select '''save file''' option.

Save dialog box opens.

Type the file name as water.mol and click on Save button.
|| Let us now save the file. 

Open the '''model kit''' menu.

Select '''save file''' option.

'''Save''' dialog box opens.

Choose a suitable location to save the file.

Type the file name as '''water.mol''' .

In '''Files of Type''' option select '''Mol.'''

Click on '''Save''' button at the bottom right corner.
|-
|| Cursor on the panel.
|| Let us open the '''2-D Editor '''in '''Jmol'''.
|-
|| Click on '''Tools''' menu, select '''2-D Editor '''from the drop-down
|| Click on''' Tools''' menu, select '''2-D Editor '''from the drop-down.

water molecule is shown in the editor.

Click on the yellow smiley button at the top left of the window.
|-
|| Cursor on the pop-up window.

Copy the '''SMILES''' string(O)for water using Ctrl and C buttons.
|| A small pop-up window opens.

Here we will see capital “'''O'''” which is the '''SMILES''' string for water molecule.

Copy the '''SMILES''' string using Ctrl and C keys.
|-
|| Click on the '''Close''' button on the '''SMILES''' window.
|| Let us close the '''SMILES''' window.
|-
|| '''Slide Number 5'''

'''Create XYZ File Format'''
|| Here we will demonstrate two ways to create XYZ file format using '''Open Babel '''.

One using '''SMILES''' string and the other using a '''mol''' file.

XYZ file format will be used to create input file to run '''ORCA'''.
|-
|| Show Openbabel interface.

[https://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html https://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html]

point to the page.
|| Open any web browser.

Type '''Openbabel '''in the '''Google''' search bar.

Click on the link '''Open Babel Chemical file format converter.'''

'''Open Babel''' page opens. 

This is an online web page to convert chemical structure files to various file formats.
|-
|| Cursor in the open babel page.
|| Let’s demonstrate how to convert a mol file and a '''SMILES '''string to '''xyz''' format.
|-
|| Inside the Input block delete the default SMILE

type the SMILE of water O or '''[OH2]. '''
|| On the left side of the page we can see an '''INPUT''' panel.

In the centre of the page you will see the '''Options''' panel.

On the right side we have an '''OUTPUT '''panel.

In the '''INPUT''' panel delete the default '''SMILE string. '''

Copy'''/'''Paste or type the SMILES string here as '''O''' for water molecule.
|-
|| Point to the''' Options''' window.

Point to the Input format - SMILES.

Select the output format as '''XYZ '''from the drop down list. 
|| In the '''Options '''panel, the input format is selected as '''SMILES'''.

Select the output format as '''XYZ '''from the drop down list. 
|-
|| In '''Generate Coordinates '''drop down, select''' 3D'''. 
|| In the '''Generate Coordinates''' drop down, select''' 3D'''. 
|-
|| Click on the “'''Convert” '''button below.

Click on the '''Convert '''button found below the '''Options''' panel.
|| Leave the other options as default.

Click on the '''Convert '''button found below the '''Options''' panel.
|-
|| Navigate to the output section on the right side of the interface. 

Click on the download File icon on the top right corner of the Output box.
|| In the '''OUTPUT''' box, '''xyz coordinates''' of the water molecule will appear. 

On the top right corner of the ''' Output '''box, click the '''Download File''' icon.
|-
|| In the Save dialog box, In the Name field, the default name '''structure.xyz '''is seen.

Change the name as water.xyz

Click on the Save button at the top right corner of the dialog box.

Show the downloading file.
|| The file downloads as '''structure.xyz''' to my '''Downloads''' folder.

Rename the file as '''water.xyz'''.

If a save file dialog box opens, save the file as '''water.xyz'''.

Back to '''Open Babel Chemical file format converter page'''.
|-
|| Point to the input box.
|| Now let’s convert a mol file to xyz format.

In the '''Open babe'''l page, on the top left side we can see '''Drop or paste here your input file ''' box.
|-
|| Click inside the box, '''File Upload''' window opens.
|| Click inside the box, ''' File Upload''' window opens.
|-
|| Point to the water.mol in the folder.

Select the saved '''water.mol''' file from the folder.

Click the '''Open''' button at the top right corner of the window.
|| Select the saved '''water.mol '''file from the folder.

Click the '''Open''' button at the top right corner of the window.
|-
|| Point to the information.

Point to the word ”string”.

Select the word''' string''' and press '''Delete key '''on the keyboard.
|| The '''INPUT''' box displays the information of the structure.

In the '''INPUT '''box, delete the first line. 

The url here. 

In some cases you may see a word “string”

This is done to avoid the url or word '''string showing up''' in the output file.
|-
|| From the '''Options '''panel, select the input format as mol--MDL MOL format.
|| From the '''Options''' panel, select the input file format as '''mol--MDL MOL''' format.
|-
|| Select the output format as xyz--XYZ cartesian coordinates format.
|| Now select the output format as xyz-'''XYZ cartesian coordinates format.'''
|-
|| In Generate Coordinates''' '''drop down, select''' 3D'''. 
|| In the '''Generate Coordinates''' drop down, select''' 3D'''. 
|-
|| Below the '''Options''' box, click on the''' Convert '''button.
|| Leave the other options as such in the panel.

Below the''' Options''' box, click on the '''Convert''' button.
|-
|| Point to the coordinates.

Navigate to the output section on the right side of the interface. 
|| In the '''OUTPUT''' box, the xyz coordinates of the water molecule are displayed.
|-
|| Click on the download File icon on the top right corner of the Output box.
|| As explained before, download the xyz file. 

Click the '''Download File''' icon in the Output box.

Save the file '''structure.xyz''' as '''water.xyz'''.
|-
|| Right-click on '''water.xyz file.'''

'''Select Open with Text Editor''' option. 
|| Let us open the''' Downloads''' folder and navigate to '''water.xyz '''.

Right-click on the file and open the file using a text editor.

Windows users may use notepad or any other text editor.
|-
|| Point to the numbers and xyz coordinates.

Point to the values.
|| The numbers in rows are the '''xyz''' coordinates of the atoms, Oxygen, Hydrogen and Hydrogen.

They are in '''Angstrom '''units.

The values here are tab separated.

We will use this''' water.xyz''' file to create the input file to run '''ORCA.'''
|-
|| '''Slide Number 6'''

'''Summary'''

In this tutorial we have learnt to,

Load water molecule in '''Jmol'''

Save the file in mol format

Create SMILES string

Create XYZ file format using''' Open Babel'''
|| With this we come to the end of this tutorial

Let us summarise.
|-
|| '''Slide Number 7'''

'''Assignment'''
|| As an assignment 
* Generate '''SMILES''' and mol file for carbon monoxide and ammonia molecules using Jmol.
* Create the '''XYZ '''files using '''SMILES''' and mol file in '''Open Babel.'''
|-
|| '''Slide Number 8'''

'''Thank you'''
|| Thank you for joining.
|-
|}