Jmol-Application/C3/Superimposing-Structures/English

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 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 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 12 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 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 4.41 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 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 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.

Contributors and Content Editors

Madhurig, Snehalathak