Difference between revisions of "Jmol-Application/C3/Superimposing-Structures/English"

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(Created page with " {|border=1 ||'''Visual Cue''' ||'''Narration''' |- ||'''Slide Number 1''' '''Title Slide''' ||Welcome to this tutorial on '''Superimposing''' '''Structures '''using '''Jmo...")
 
 
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 +
'''Title of script''': '''Superimposing Structures '''
 +
 +
'''Author: '''Dr. Snehalatha Kaliappan
 +
 +
'''Keywords: '''  jmol, superimposing structures, stereoisomers, script commands, compare command word, translate model, rotate model, append model,  cahn-ingold-prelog priority rules, r/s configuration, rmsd score, video tutorial.
  
  
Line 36: Line 41:
 
||Here I am using
 
||Here I am using
  
−
'''Ubuntu Linux '''OS version 20.04
+
'''Ubuntu Linux ''' OS version 20.04
  
−
Jmol version 14.32.80
+
'''Jmol''' version 14.32.80
  
−
Java version 11.0.16
+
'''Java''' version 11.0.16
  
 
A working Internet connection.
 
A working Internet connection.
Line 51: Line 56:
 
||To follow this tutorial, learner should be familiar with,
 
||To follow this tutorial, learner should be familiar with,
  
−
Chemistry topics from undergraduate courses.
+
Chemistry topics from undergraduate courses and
  
−
Basic operations of Jmol.
+
Basic operations of '''Jmol'''.
  
 
|-
 
|-
Line 63: Line 68:
 
'''https://spoken-tutorial.org/tutorial-search/?search_foss=Jmol+Application&search_language=English'''
 
'''https://spoken-tutorial.org/tutorial-search/?search_foss=Jmol+Application&search_language=English'''
  
−
||For the prerequisite Jmol tutorials please visit this website.
+
||For the prerequisite '''Jmol''' tutorials please visit this website.
  
 
|-
 
|-
Line 103: Line 108:
  
  
−
Type '''lactic acid '''in the search field and click on '''OK''' button.
+
Type '''lactic acid ''' in the search field and click on '''OK''' button.
  
 
|-
 
|-
Line 115: Line 120:
 
It is attached to 4 different groups.
 
It is attached to 4 different groups.
  
−
It exists as two enantiomers
+
It exists as two '''enantiomers'''.
  
 
|-
 
|-
Line 124: Line 129:
  
  
−
[[Image:image1.png.png|top]]
 
 
||L-Lactic acid , (''S'')-lactic acid, or (+)-lactic acid), and D-Lactic acid, (''R'')-lactic acid, or (−)-lactic acid)
 
||L-Lactic acid , (''S'')-lactic acid, or (+)-lactic acid), and D-Lactic acid, (''R'')-lactic acid, or (−)-lactic acid)
  
Line 139: Line 143:
 
The groups around the central carbon atom are arranged anticlockwise.
 
The groups around the central carbon atom are arranged anticlockwise.
  
−
Hence, this model is of '''S-lactic acid.'''
+
Hence, this model is of '''S-lactic acid'''.
  
 
Please go through the additional reading material for more information.
 
Please go through the additional reading material for more information.
Line 150: Line 154:
 
|-
 
|-
  
−
||Click on the '''modelkit''' icon and from the menu select '''Save file''' option.  
+
||Click on the '''modelkit''' icon  
 +
 
 +
and from the menu select '''Save file''' option.  
  
 
Type '''S-lacticacid.mol '''File Name field.
 
Type '''S-lacticacid.mol '''File Name field.
Line 196: Line 202:
  
 
Click on the hydrogen atom.  
 
Click on the hydrogen atom.  
−
||Open the '''modelkit '''menu, make sure that carbon is selected in the elements list.
+
||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.
 
Click on the hydrogen atom to replace it with the methyl group.
Line 217: Line 223:
 
||We have now swapped the positions of hydrogen and methyl groups.
 
||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.
+
Let us rotate the model in such a way that hydrogen is at the back of the central carbon atom.
  
 
|-
 
|-
Line 224: Line 230:
  
  
−
This is a model of '''R-lactic acid.'''
+
This is a model of '''R-lactic acid'''.
  
 
|-
 
|-
−
||Click on the '''modelkit '''icon and from the menu select '''Save file''' option.  
+
||Click on the '''modelkit '''icon.
 +
 
 +
from the menu select '''Save file''' option.  
  
  
Line 241: Line 249:
 
This can be achieved by different methods.
 
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.
+
 
 +
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.
 
Open the '''Console''' using the '''File''' menu.
Line 249: Line 259:
  
  
−
We will load the already saved model of '''S-Lactic acid.'''
+
We will load the already saved model of '''S-Lactic acid'''.
  
 
|-
 
|-
Line 263: Line 273:
 
'''Load append '''
 
'''Load append '''
  
−
followed by the name of the saved mol file for S-lactic acid, '''S-lacticacid.mol'''
+
followed by the name of the saved mol file for S-lactic acid, '''S-lacticacid.mol'''.
  
 
Press '''Enter'''.
 
Press '''Enter'''.
Line 287: Line 297:
  
 
From the options select “'''drag molecule”''' option.
 
From the options select “'''drag molecule”''' option.
 +
 +
Click on Close(x) button.
  
 
||Both the models are displayed on the panel together.
 
||Both the models are displayed on the panel together.
  
 
We have to separate them.  
 
We have to separate them.  
 +
 +
Close the '''console''' window.
  
 
Open the '''modelkit''' menu.
 
Open the '''modelkit''' menu.
Line 326: Line 340:
 
|-
 
|-
  
−
||Click on one structure, drag and put the structure over the other.  
+
||Click on one structure,  
 +
 
 +
drag and put the structure over the other.  
 
||Let us check if they are indeed non-superimposable.  
 
||Let us check if they are indeed non-superimposable.  
  
Line 340: Line 356:
 
||Open the '''modelkit '''menu.
 
||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.
 
Click on any atom on any model and drag.
Line 347: Line 363:
  
 
|-
 
|-
−
||'''Slide Number 10'''
+
||'''Slide Number 10 and 11'''
  
  
 
'''Script Command'''
 
'''Script Command'''
−
||Script command with '''Compare''' command word can be used for superimposition
+
||Script command with '''Compare''' command word can be used for superimposition.
  
  
Line 359: Line 375:
  
 
|-
 
|-
−
||'''Slide number 11'''
+
||'''Slide number 12'''
  
  
 
'''Script Command'''
 
'''Script Command'''
 +
 +
'''compare {model1} {model2} SMARTS or SMILES "smartsString" translate rotate'''
 +
 +
 +
'''https://chemapps.stolaf.edu/jmol/docs/#compare'''
 +
 
||The command line with following syntax will be used for the purpose
 
||The command line with following syntax will be used for the purpose
  
  
−
'''compare {model1} {model2} SMARTS or SMILES "smartsString" translate rotate'''
+
'''compare {model1} {model2} SMARTS or SMILES "smartsString" translate rotate'''.
  
 
Please use the link below to know more about '''Compare''' command.
 
Please use the link below to know more about '''Compare''' command.
  
−
'''https://chemapps.stolaf.edu/jmol/docs/#compare'''
 
  
 
|-
 
|-
−
||'''Slide number 12'''
+
||'''Slide number 13'''
  
  
Line 379: Line 400:
  
 
'''Compare {2.1} {1.1} SMARTS “O=COH” translate rotate 2.0'''.
 
'''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.
+
||I have modified the above command line as shown here to suit our purpose.
  
−
Here, '''Compare''' word is followed by the model number.  
+
Here, '''compare''' word is followed by the model number.  
  
 
We have loaded 2 models on the panel, D lactic acid and L-lactic acid.
 
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.
+
1.1 refers to the first model in the file and 2.1 refers to the second model in the file.
  
 
|-
 
|-
Line 396: Line 417:
 
The string of atoms to be compared are in double quotes.
 
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.  
+
These are atoms in the first structure that correlate one-to-one with atoms in the second structure.  
  
 
Then find the rotation and translation that best aligns them.  
 
Then find the rotation and translation that best aligns them.  
Line 411: Line 432:
  
 
Press '''Enter'''
 
Press '''Enter'''
−
||Open the '''console''' using the file menu.
+
||Open the '''console''' using the File menu.
  
 
Type the compare command as shown here in the '''console''' window.
 
Type the compare command as shown here in the '''console''' window.
Line 424: Line 445:
 
||On the console window you will see a message in blue.  
 
||On the console window you will see a message in blue.  
  
−
It shows the RMSD score for this superposition.
+
It shows the RMSD score for the'''Bold text''' superposition.
  
 
|-
 
|-
−
||'''Slide Number 13'''
+
||'''Slide Number 14'''
  
  
Line 438: Line 459:
  
 
|-
 
|-
−
||'''Slide Number 14'''
+
||'''Slide Number 15'''
  
  
Line 449: Line 470:
 
|-
 
|-
 
||Cursor on the console.
 
||Cursor on the console.
−
||Here, '''RMSD''' score of 4.10 angstroms indicates dissimilar structures.
+
||Here, '''RMSD''' score of 4.41 angstroms indicates dissimilar structures.
  
 
The '''RMSD''' score can vary slightly for the learners.
 
The '''RMSD''' score can vary slightly for the learners.
Line 456: Line 477:
  
 
|-
 
|-
−
||'''Slide number 15'''
+
||'''Slide number 16'''
  
  
Line 462: Line 483:
 
||We will compare the structures of 3 simple carbohydrates,  
 
||We will compare the structures of 3 simple carbohydrates,  
  
−
D-altrose, D-glucose, and D-mannose
+
D-Altrose, D-Glucose, and D-Mannose
  
 
Their structures resemble very closely with each other.
 
Their structures resemble very closely with each other.
Line 472: Line 493:
 
|-
 
|-
 
||Click on the '''File''' menu and select '''New''' option.
 
||Click on the '''File''' menu and select '''New''' option.
−
||I will open a new Jmol window.  
+
||I will open a new '''Jmol''' window.  
  
  
Line 487: Line 508:
 
||On the toolbar, click on '''Open a file''' tool.
 
||On the toolbar, click on '''Open a file''' tool.
  
−
'''Open''' dialog box opens. Select the saved input file for '''D-glucose.mol'''.
+
'''Open''' dialog box opens.  
 +
 
 +
Select the saved input file for '''D-glucose.mol'''.
  
 
Click on the '''Open''' button.
 
Click on the '''Open''' button.
Line 502: Line 525:
  
 
Click on the '''Open''' button.
 
Click on the '''Open''' button.
−
||To load the 2nd model, click on the '''Open a file''' tool.
+
||To load the second model, click on the '''Open a file''' tool.
  
 
Once again the '''Open''' dialog box opens.
 
Once again the '''Open''' dialog box opens.
  
−
Select '''D-altrose.mol.'''  
+
Select '''D-altrose.mol'''.
  
  
Line 528: Line 551:
  
 
Click on the '''Open''' button
 
Click on the '''Open''' button
−
||Similarly, '''load''' and '''append''' the model of '''D-mannose '''on the panel.
+
||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.
 
||Click on '''All frames '''tool on the far right end of the tool bar.
Line 543: Line 566:
 
Click on the models and drag.
 
Click on the models and drag.
  
−
||Separate the models on the panel using '''drag molecule''' option in the '''modelkit. '''
+
||Separate the models on the panel using '''drag molecule''' option in the '''modelkit'''.
  
 
Place the models as shown here.
 
Place the models as shown here.
Line 567: Line 590:
 
||At the prompt type the following command.
 
||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.
 
Here we are comparing model 1 and 2.
Line 573: Line 595:
 
Model 1 is '''D-glucose''' and model 2 is '''D-altrose'''.
 
Model 1 is '''D-glucose''' and model 2 is '''D-altrose'''.
  
−
We are using the '''SMILES,''' which means we are comparing the whole molecule.
+
We are using the '''SMILES''', which means we are comparing the whole molecule.
  
 
Press '''Enter'''.
 
Press '''Enter'''.
Line 582: Line 604:
 
||The models are superimposed on each other.
 
||The models are superimposed on each other.
  
−
The '''RMSD''' score of '''0.79''' '''angstroms''' is displayed on the console.
+
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.
+
||Click on '''drag molecule''' option in the modelkit.  
−
||Let’s separate the superimposed models.
+
 
−
Use the '''drag molecule''' option in the '''modelkit''' and separate  
+
Click on the model and drag.
 +
||Let us separate the superimposed models.
 +
 
 +
Use the '''drag molecule''' option in the '''modelkit''' menu to separate the models.
 
|-
 
|-
 
||Press up arrow key.  
 
||Press up arrow key.  
Line 615: Line 640:
 
The '''RMSD''' score for this superposition is 0.638 angstroms.
 
The '''RMSD''' score for this superposition is 0.638 angstroms.
  
−
This value is slightly lower than for '''D-glucose''' and '''D-altrose'''.
+
This value is slightly lower than that for '''D-glucose''' and '''D-altrose'''.
 
|-
 
|-
 
||Click on '''drag molecule''' option in the modelkit. Click on the model and drag.
 
||Click on '''drag molecule''' option in the modelkit. Click on the model and drag.
Line 626: Line 651:
 
'''Compare {2.1} {3.1}SMILES translate rotate 2.0'''
 
'''Compare {2.1} {3.1}SMILES translate rotate 2.0'''
  
−
||On the console, Press up arrow key and edit the command as follows.
+
||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.
 
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'''.
 
||Press '''Enter'''.
Line 643: Line 667:
 
Now models 2 and 3 are superimposed.
 
Now models 2 and 3 are superimposed.
  
−
These are models of '''D-altrose ''' and '''D-mannose.'''
+
These are models of '''D-altrose ''' and '''D-mannose'''.
  
 
The '''RMSD''' score here is 0.578 angstroms.
 
The '''RMSD''' score here is 0.578 angstroms.
Line 650: Line 674:
  
 
By Mlicuana - Own work, Public Domain, https://commons.wikimedia.org/w/index.php?curid=12116368
 
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.
+
||Structures of '''D-altrose ''' and '''D-mannose''' resemble more closely when compared to other pairs.
  
 
Pairs of structures, '''D-glucose''', '''D-mannose''' and '''D-altrose, D-mannose '''are '''epimers'''.
 
Pairs of structures, '''D-glucose''', '''D-mannose''' and '''D-altrose, D-mannose '''are '''epimers'''.
Line 657: Line 681:
  
 
|-
 
|-
−
||'''Slide Number 16'''
+
||'''Slide Number 17'''
  
 
'''Summary slide'''
 
'''Summary slide'''
Line 664: Line 688:
 
In this tutorial, we learned to,
 
In this tutorial, we learned to,
  
−
* Load two or more models on the Jmol panel.
+
* Load two or more models on the '''Jmol''' panel.
  
 
* Translate and rotate models on the panel.
 
* Translate and rotate models on the panel.
  
 
|-
 
|-
−
||'''Slide Number 17'''
+
||'''Slide Number 18'''
  
 
'''Summary slide'''
 
'''Summary slide'''
−
||* Superimpose models using script commands.
+
||
 +
* Superimpose models using script commands.
  
−
* Compared the RMSD score for the superimposition.
+
* Compared the '''RMSD''' score for the superimposition.
  
 
|-
 
|-
−
||'''Slide Number 18'''
+
||'''Slide Number 19'''
  
 
'''Assignment'''
 
'''Assignment'''
Line 684: Line 709:
 
Explore the '''compare''' command and superimpose models of your choice.
 
Explore the '''compare''' command and superimpose models of your choice.
 
|-
 
|-
−
||'''Slide Number 19'''
+
||'''Slide Number 20'''
  
  
Line 692: Line 717:
 
* Please download and watch it.  
 
* Please download and watch it.  
 
|-
 
|-
−
||'''Slide Number 20'''
+
||'''Slide Number 21'''
  
  
Line 698: Line 723:
 
||
 
||
 
* We conduct workshops using spoken tutorials and give certificates.  
 
* We conduct workshops using spoken tutorials and give certificates.  
 +
 
* For more details, please contact us.  
 
* For more details, please contact us.  
  
  
 
|-
 
|-
−
||'''Slide Number 21'''
+
||'''Slide Number 22'''
  
  
Line 720: Line 746:
  
 
|-
 
|-
−
||'''Slide''' '''Number 22'''
+
||'''Slide''' '''Number 23'''
  
  
Line 727: Line 753:
 
|-
 
|-
 
||  
 
||  
−
||The script for this tutorial is contributed by Snehalatha Kaliappan, This is Madhuri Ganapathi from IIT Bombay signing off.  
+
||The script for this tutorial is contributed by Snehalatha Kaliappan.
 +
 
 +
This is Madhuri Ganapathi from IIT Bombay signing off.  
  
 
Thank you for joining.  
 
Thank you for joining.  
 
|-
 
|-
 
|}
 
|}

Latest revision as of 16:54, 20 March 2023

Title of script: Superimposing Structures

Author: Dr. Snehalatha Kaliappan

Keywords: jmol, superimposing structures, stereoisomers, script commands, compare command word, translate model, rotate model, append model, cahn-ingold-prelog priority rules, r/s configuration, rmsd score, video tutorial.


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 and

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


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 us 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.

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.

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.

Click on Close(x) button.

Both the models are displayed on the panel together.

We have to separate them.

Close the console window.

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 drag 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 and 11


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 12


Script Command

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


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

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.


Slide number 13


Script Command

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

I have modified the above command line as shown here 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 first model in the file and 2.1 refers to the second 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 the first 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 theBold text superposition.

Slide Number 14


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 15


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 4.41 angstroms indicates dissimilar structures.

The RMSD score can vary slightly for the learners.

Let me demonstrate this with one more example.

Slide number 16


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 second 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.


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 us separate the superimposed models.

Use the drag molecule option in the modelkit menu to separate the models.

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 that 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.


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 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 17

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 18

Summary slide

  • Superimpose models using script commands.
  • Compared the RMSD score for the superimposition.
Slide Number 19

Assignment

Here is an assignment for you,

Explore the compare command and superimpose models of your choice.

Slide Number 20


About Spoken Tutorial Project

  • The video at the following link summarizes the Spoken Tutorial project.
  • Please download and watch it.
Slide Number 21


Spoken tutorial workshops

  • We conduct workshops using spoken tutorials and give certificates.
  • For more details, please contact us.


Slide Number 22


Answers for THIS Spoken Tutorial

  • Do you have questions in THIS Spoken Tutorial?
  • Please visit this site
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Slide Number 23


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.

Contributors and Content Editors

Madhurig, Snehalathak

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