Snehalathak at 11:24, 20 March 2023

2023-03-20T11:24:08Z

Madhurig at 07:22, 20 March 2023

2023-03-20T07:22:03Z

Madhurig at 07:17, 20 March 2023

2023-03-20T07:17:49Z

Madhurig at 07:16, 20 March 2023

2023-03-20T07:16:18Z

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Snehalathak at 09:34, 17 March 2023

2023-03-17T09:34:58Z

Snehalathak: Created page with " {|border=1 ||'''Visual Cue''' ||'''Narration''' |- ||'''Slide Number 1''' '''Title Slide''' ||Welcome to this tutorial on '''Superimposing''' '''Structures '''using '''Jmo..."

2023-03-17T09:32:36Z

Created page with " {|border=1 ||'''Visual Cue''' ||'''Narration''' |- ||'''Slide Number 1''' '''Title Slide''' ||Welcome to this tutorial on '''Superimposing''' '''Structures '''using '''Jmo..."

New page

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

||'''Slide Number 1'''

'''Title Slide'''
||Welcome to this tutorial on '''Superimposing''' '''Structures '''using '''Jmol'''.

|-
||'''Slide Number 2'''

'''Learning Objectives'''
||In this tutorial, we will learn to,

* Load two or more models on the Jmol panel.

* Translate and rotate models on the panel.

|-
||'''Slide Number 3'''

'''Learning Objectives'''
||
* Superimpose models using script commands.

* Compare RMSD score for the superimposition.
|-
||'''Slide Number 4'''

'''System Requirement'''
||Here I am using

'''Ubuntu Linux '''OS version 20.04

Jmol version 14.32.80

Java version 11.0.16

A working Internet connection.

|-
||'''Slide Number 5'''

'''Pre-requisites'''

||To follow this tutorial, learner should be familiar with,

Chemistry topics from undergraduate courses.

Basic operations of Jmol.

|-
||'''Slide Number 6'''

'''Pre-requisites'''

'''https://spoken-tutorial.org/tutorial-search/?search_foss=Jmol+Application&search_language=English'''

||For the prerequisite Jmol tutorials please visit this website.

|-
||'''Slide Number 7'''

'''Code Files '''
||
* The input files required for this tutorial are available in the '''Code files''' link.

* Please download and extract the files.

* Make a copy of all the files and then use them for practising.

|-
||'''Slide Number 8'''

'''Significance of Comparing 3D structures '''

||Comparing 3D structures of molecules is useful in,

* Stereochemical analysis

* Predicting molecular functions

* Drug discovery and design of ligands

|-
||Cursor on Jmol window.
||Here I have opened the '''Jmol''' interface.

Let us begin by comparing structures of simple organic molecule, lactic acid.
|-
||Open the '''File''' menu and select '''Get Mol''' option.
||We will load the model of lactic acid from the database.

Open the '''File''' menu and select '''Get Mol''' option.

Type '''lactic acid '''in the search field and click on '''OK''' button.

|-
||Cursor on the lactic acid model on Jmol interface.

Rotate the model to show the central carbon atom.
||The model of lactic acid is displayed on the screen.

The central carbon in lactic acid is chiral.

It is attached to 4 different groups.

It exists as two enantiomers

|-
||'''Slide Number 9'''

'''Enantiomers of Lactic Acid'''

[[Image:image1.png.png|top]]
||L-Lactic acid , (''S'')-lactic acid, or (+)-lactic acid), and D-Lactic acid, (''R'')-lactic acid, or (−)-lactic acid)

These two molecules are non-superimposable mirror images of each other.

|-
||Click on the rotate molecule icon in the tools menu. Click on the model and drag to rotate.

Cursor on the central carbon atom.
||Let us assign the R and S configurations using '''Cahn-Ingold-Prelog''' priority rules.

Rotate the model such that the hydrogen is at the back of the central carbon.

The groups around the central carbon atom are arranged anticlockwise.

Hence, this model is of '''S-lactic acid.'''

Please go through the additional reading material for more information.

|-

||Cursor on the panel.
||Let us save this model.

|-

||Click on the '''modelkit''' icon and from the menu select '''Save file''' option.

Type '''S-lacticacid.mol '''File Name field.

Select the '''Files of type''' as '''Mol'''.

Click on '''Save''' button.

||Click on the '''modelkit''' icon and from the menu select '''Save file '''option.

'''Save '''dialog-box opens.

I am saving this file to the '''Jmol''' folder where the '''Jmol.jar''' file is located.

Details on how to change the default directory can be found in the '''additional reading material'''.

I will name the file as '''S-lacticacid.mol'''.

Select the '''Files of type''' as '''Mol'''.

Click on '''Save''' button.

|-

||Cursor on the model.
||Now let us convert the '''S-Lactic acid''' model into '''R-Lactic acid'''.

|-
||Cursor on the model.
||For this we need to break the bonds and reconnect the bonds.

We can swap the position of any two groups to create the model of '''R-lactic acid'''.

|-
||Point to hydrogen atom and methyl group
||Let’s keep it simple.

I will choose to swap the positions of the hydrogen atom and methyl group.

|-

||Open the '''modelkit''' menu.

Click on the hydrogen atom.
||Open the '''modelkit '''menu, make sure that carbon is selected in the elements list.

Click on the hydrogen atom to replace it with the methyl group.

|-
||Open the''' modelkit''' menu, select hydrogen from the elements list.

Click on the carbon atom of the methyl group.
||Now open the '''modelkit''' menu, select hydrogen from the elements list.

Click on the carbon atom of the methyl group to replace it with hydrogen.

|-
||Cursor on hydrogen and methyl groups

Rotate the model.
||We have now swapped the positions of hydrogen and methyl groups.

Let’s rotate the model in such a way that hydrogen is at the back of the central carbon atom.

|-
||Cursor on the groups.
||Now after assigning the priority, the groups are in clockwise direction.

This is a model of '''R-lactic acid.'''

|-
||Click on the '''modelkit '''icon and from the menu select '''Save file''' option.

Type '''R-lacticacid.mol '''File Name field.

Select the '''Files of type''' as '''Mol'''.

Click on '''Save''' button.
||As demonstrated before, let’s save the model on the panel as '''R-lacticacid.mol'''.

To compare the isomers of lactic acid, we need to load both the models on the panel.

This can be achieved by different methods.
|-
||Click on the '''File''' menu and select the '''Console''' option.
||First, I will type the script commands on the console to load the models.

Open the '''Console''' using the '''File''' menu.

I will resize the console to see the models clearly.

We will load the already saved model of '''S-Lactic acid.'''

|-
||At the prompt type,

'''Load append S-lacticacid.mol'''

Press '''Enter'''.

Point to the output.
||On the '''console''' window, at the prompt type,

'''Load append '''

followed by the name of the saved mol file for S-lactic acid, '''S-lacticacid.mol'''

Press '''Enter'''.

'''Console''' shows 2 models.
|-
||At the prompt type,

'''frame all'''

Press '''Enter'''.

||To view both the molecules on the screen type the command,

'''frame all'''

Press '''Enter'''.

|-
||Cursor on the panel.

Open the '''modelkit menu'''.

From the options select “'''drag molecule”''' option.

||Both the models are displayed on the panel together.

We have to separate them.

Open the '''modelkit''' menu.

From the options select '''drag molecule''' option.
|-
||Place the cursor on any atom of any model.

Hold the left mouse button and drag the mouse.
||Place the cursor on any atom of any model.

Hold the left mouse button and drag the mouse.

Place the model next to the other model.

Leave the hold on the mouse button.
|-
||Place the mouse on the model.

Hold the '''Alt''' button and left mouse button and drag.
||To rotate the model, place the mouse cursor on the model.

Press the '''Alt''' button and left mouse button and drag.
|-
||Rotate the model.
||I will adjust the models in such a way that they look like mirror images of each other.

|-
||Cursor on the panel.
||These two structures are enantiomers.

They are non-superimposable mirror images.
|-

||Click on one structure, drag and put the structure over the other.
||Let us check if they are indeed non-superimposable.

We can manually superimpose one structure over the other.

Click on one structure, drag and put the structure over the other.

As you can see clearly the groups other than hydrogen are not aligned.

Hence they are non-superimposable.

|-
||Open the '''modelkit '''menu.

From the options select ```dr'ag molecule’’’ option.

Click on any atom on any model and drag.

||Let us separate the models and look at other options to superimpose.

|-
||'''Slide Number 10'''

'''Script Command'''
||Script command with '''Compare''' command word can be used for superimposition

The command compares two models and re-orients the first model relative to the second

The re-orientation is based on the given atom-atom coordinate pairing

|-
||'''Slide number 11'''

'''Script Command'''
||The command line with following syntax will be used for the purpose

'''compare {model1} {model2} SMARTS or SMILES "smartsString" translate rotate'''

Please use the link below to know more about '''Compare''' command.

'''https://chemapps.stolaf.edu/jmol/docs/#compare'''

|-
||'''Slide number 12'''

'''Script Command'''

'''Compare {2.1} {1.1} SMARTS “O=COH” translate rotate 2.0'''.
||I have modified the above command line as below to suit our purpose.

Here, '''Compare''' word is followed by the model number.

We have loaded 2 models on the panel, D lactic acid and L-lactic acid.

1.1 refers to the 1st model in the file and 2.1 refers to the 2nd model in the file.

|-
||Cursor on Slide Number 10

Cursor on the words on the command syntax.
||'''SMARTS''' refers to the substructure description.

The string of atoms to be compared are in double quotes.

These are atoms in one structure that correlate one-to-one with atoms in the second structure.

Then find the rotation and translation that best aligns them.

2.0 refers to the number of seconds to complete the translation and rotation animation.

You can change the number here as per your preference.
|-
||Cursor on the console window.

Type,

'''Compare {2.1} {1.1} SMARTS “O=COH” translate rotate 2.0'''

Press '''Enter'''
||Open the '''console''' using the file menu.

Type the compare command as shown here in the '''console''' window.

Press '''Enter'''.
|-
||Cursor on the panel.
||The two structures are now superimposed.
|-
|| Point to the message in blue.
||On the console window you will see a message in blue.

It shows the RMSD score for this superposition.

|-
||'''Slide Number 13'''

'''RMSD score'''
||'''root-mean-square deviation (RMSD)''':

It is the measure of the average distance between the atoms of superimposed models.

It is measured in angstrom units.

|-
||'''Slide Number 14'''

'''RMSD score'''
||The smaller the RMSD value, the more similar the two structures.

An''' RMSD '''score of less than 2.0 angstroms is observed when the structures have good superposition.

|-
||Cursor on the console.
||Here, '''RMSD''' score of 4.10 angstroms indicates dissimilar structures.

The '''RMSD''' score can vary slightly for the learners.

Let me demonstrate this with one more example.

|-
||'''Slide number 15'''

'''Structures of Carbohydrates'''
||We will compare the structures of 3 simple carbohydrates,

D-altrose, D-glucose, and D-mannose

Their structures resemble very closely with each other.

The mol files for the models are shared in the code files folder.

Please download and use them as input files.

|-
||Click on the '''File''' menu and select '''New''' option.
||I will open a new Jmol window.

Another way to load and append the models on panel is by using the toolbar.
|-
||On the tool bar, click on '''Open a file''' tool.

In '''Open''' dialog box, select the saved input file for '''D-glucose.mol'''.

Click on the '''Open''' button.

Cursor on the model.
||On the toolbar, click on '''Open a file''' tool.

'''Open''' dialog box opens. Select the saved input file for '''D-glucose.mol'''.

Click on the '''Open''' button.

The model of open chain '''D-glucose''' is displayed on the screen.
|-
||Click on the '''Open a file''' tool.

In the '''Open''' dialog box, select '''D-altrose.mol'''.

Check the checkbox for '''Append models'''.

Uncheck the '''PDB cartoons''' checkbox.

Click on the '''Open''' button.
||To load the 2nd model, click on the '''Open a file''' tool.

Once again the '''Open''' dialog box opens.

Select '''D-altrose.mol.'''

Check the checkbox for '''Append models'''.

This check box is available on the right-side of the '''Open''' dialog box.

Uncheck the other checkboxes if they are checked.

Click on the '''Open''' button.

The model of '''D-altrose''' is displayed on the screen.
|-
||Click on the '''Open a file''' tool.

In the '''Open''' dialog box, select '''D-mannose.mol.'''

Check the checkbox for '''Append models'''.

Uncheck the '''PDB cartoons''' checkbox.

Click on the '''Open''' button
||Similarly, '''load''' and '''append''' the model of '''D-mannose '''on the panel.
|-
||Click on '''All frames '''tool on the far right end of the tool bar.

Cursor on the models.
||To view them all in one frame, click on '''All frames '''tool on the far right end of the tool bar.

The 3 models appear superimposed on each other.
|-
||Cursor on the panel.

Open''' modelkit '''menu and select''' drag molecule''' option.

Click on the models and drag.

||Separate the models on the panel using '''drag molecule''' option in the '''modelkit. '''

Place the models as shown here.

|-
||Cursor on the panel.

Click on the File menu and select '''Console'''.
||Let us compare the models with one another.

The '''RMSD''' score for the comparison will allow us to determine which carbohydrates are similar.

Open the console using the '''File''' menu.
|-
||Drag to resize the console window.
||I will resize the console window to see the superimposing clearly.
|-
||At the prompt type the following command.

'''Compare {2.1} {1.1}SMILES translate rotate 2.0'''

Press '''Enter'''.
||At the prompt type the following command.

'''Compare {2.1} {1.1}SMILES translate rotate 2.0'''

Here we are comparing model 1 and 2.

Model 1 is '''D-glucose''' and model 2 is '''D-altrose'''.

We are using the '''SMILES,''' which means we are comparing the whole molecule.

Press '''Enter'''.
|-
||Cursor on the panel.

Cursor on the console.
||The models are superimposed on each other.

The '''RMSD''' score of '''0.79''' '''angstroms''' is displayed on the console.
|-
||Click on '''drag molecule''' option in the modelkit. Click on the model and drag.
||Let’s separate the superimposed models.
Use the '''drag molecule''' option in the '''modelkit''' and separate
|-
||Press up arrow key.

Edit command as follows.

'''Compare {3.1} {1.1}SMILES translate rotate 2.0'''

Press '''Enter'''.
||Press up arrow key to get the previous command at the prompt.

Edit the number for the model as 3.1 in place of 2.1.

Here we want to compare model 3 with model 1.

Model 3 is ''' D-mannose''' and model 1 is '''D-glucose'''.

Press '''Enter'''.
|-
||Cursor on the panel.

Cursor on the console RMSD score.

||Models of '''D-mannose''' and '''D-glucose''' are superimposed on the panel.

The '''RMSD''' score for this superposition is 0.638 angstroms.

This value is slightly lower than for '''D-glucose''' and '''D-altrose'''.
|-
||Click on '''drag molecule''' option in the modelkit. Click on the model and drag.

||Again separate the models on the panel.

|-
||Press up arrow key. Edit command as follows.

'''Compare {2.1} {3.1}SMILES translate rotate 2.0'''

||On the console, Press up arrow key and edit the command as follows.

Edit the number for the model as 2.1 instead of 1.1.

'''Compare {2.1} {3.1}SMILES translate rotate 2.0'''
|-
||Press '''Enter'''.

Cursor on the panel.

Cursor on the '''console RMSD score'''.
||Press '''Enter'''.

Now models 2 and 3 are superimposed.

These are models of '''D-altrose ''' and '''D-mannose.'''

The '''RMSD''' score here is 0.578 angstroms.
|-
||Point to the structures.

By Mlicuana - Own work, Public Domain, https://commons.wikimedia.org/w/index.php?curid=12116368
||Structures of '''D-altrose ''' and '''D-mannose''' resemble more closely when compared to the other pairs.

Pairs of structures, '''D-glucose''', '''D-mannose''' and '''D-altrose, D-mannose '''are '''epimers'''.

The pair of structures, '''D-glucose, D-altrose ''' are '''diastereomers'''.

|-
||'''Slide Number 16'''

'''Summary slide'''
||Let's Summarize.

In this tutorial, we learned to,

* Load two or more models on the Jmol panel.

* Translate and rotate models on the panel.

|-
||'''Slide Number 17'''

'''Summary slide'''
||* Superimpose models using script commands.

* Compared the RMSD score for the superimposition.

|-
||'''Slide Number 18'''

'''Assignment'''
||Here is an assignment for you,

Explore the '''compare''' command and superimpose models of your choice.
|-
||'''Slide Number 19'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.
|-
||'''Slide Number 20'''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please contact us.

|-
||'''Slide Number 21'''

'''Answers for THIS Spoken Tutorial '''

* Do you have questions in THIS Spoken Tutorial?
* Please visit this site
* Choose the minute and second where you have the question.
* Explain your question briefly
* The spoken tutorial project will ensure answer.
* You will have to register on this website to ask questions.

||
* Please post your timed queries in this forum,

|-
||'''Slide''' '''Number 22'''

'''Acknowledgement '''
||Spoken Tutorial project is funded by Ministry of Education (MoE), Govt. of India
|-
||
||The script for this tutorial is contributed by Snehalatha Kaliappan, This is Madhuri Ganapathi from IIT Bombay signing off.

Thank you for joining.
|-
|}

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 '''Summary slide'''
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 '''Assignment'''
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 Explore the '''compare''' command and superimpose models of your choice.
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 * Please download and watch it.
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@@ Line 154: / Line 154: @@
 |-
-||Click on the '''modelkit''' icon and from the menu select '''Save file''' option.
+||Click on the '''modelkit''' icon
 Type '''S-lacticacid.mol '''File Name field.
@@ Line 231: / Line 233: @@
 |-
-||Click on the '''modelkit '''icon and from the menu select '''Save file''' option.
+||Click on the '''modelkit '''icon.
@@ Line 245: / Line 249: @@
 This can be achieved by different methods.
 |-
-||Click on the '''File''' menu and select the '''Console''' option.
+||Click on the '''File''' menu.
 ||First, I will type the script commands on the '''console''' to load the models.
@@ Line 334: / Line 340: @@
 |-
-||Click on one structure, drag and put the structure over the other.
+||Click on one structure,
 ||Let us check if they are indeed non-superimposable.
@@ Line 348: / Line 356: @@
 ||Open the '''modelkit '''menu.
-From the options select ```dr'ag molecule’’’ option.
+From the options select '''drag molecule''' option.
 Click on any atom on any model and drag.

@@ Line 127: / Line 127: @@
 '''Enantiomers of Lactic Acid'''
-[[Image:image1.png.png|top]]
 ||L-Lactic acid , (''S'')-lactic acid, or (+)-lactic acid), and D-Lactic acid, (''R'')-lactic acid, or (−)-lactic acid)