Welcome to this tutorial on Structures from Database in Jmol.
In this tutorial, we will learn to:
Load chemical structures from PubChem database and
Convert 2D structures drawn in GChemPaint to 3D models in Jmol.
To follow this tutorial, you should be familiar with Jmol Application.
If not, watch the relevant tutorials available at our website.
To record this tutorial, I am using:
Ubuntu OS version 12.04
Jmol version 12.2.2
Java version 7
GChemPaint version 0.12.10
Mozilla Firefox browser 22.0.
I have opened a new Jmol Application window.
Jmol has a feature to load structures of compounds listed in the database.
The File' menu on the menu bar has an option Get MOL.
This loads molecules from chemical structure database PubChem.
It also has another option Get PDB to load protein structures from Protein Data Bank.
This feature will be explained in detail, in another tutorial.
To load a chemical structure on the panel, click on Get Mol.
An Input dialog-box opens on the screen.
Any molecule listed in the database can be loaded by typing the following, in the text box:
Common name or IUPAC name,
CAS number,
CID number,
InChi identifier or
SMILES identifier.
Please visit Pubchem database website for information on identification numbers, for a particular chemical.
Let us display phenol on screen.
So, type: "phenol" in the Input text-box.
click on OK button.
A model of phenol is displayed on the panel.
We can modify the display of phenol using various rendering options.
These options are listed in the Menu bar and Pop-up menu.
We can add substituents to the benzene ring of phenol.
First, let us label the atoms in the model.
Click on the Display menu and select Label. Click on Number option.
Now, let's replace a hydrogen- number 10, attached to the carbon atom -number 4, with an amino group.
Open the modelkit menu, select nitrogen from the options.
Click on hydrogen- number 10.
This is a molecule of Para-Amino Phenol on the panel.
We will change the display to Sticks display.
Exit the modelkit menu.
Open the Pop-up menu, scroll down to Style , select Scheme and click on Sticks options.
On the panel, we have a model of Para-Amino-phenol in sticks display.
Complex structures which are difficult to create, can easily be loaded on the panel.
For example: cholesterol.
Click on File menu.
Click on Get Mol option. In the text-box, type: Cholesterol .
click on OK button.
A molecule of Cholesterol is displayed on the panel.
We can highlight the features like double-bond and side-chain, in the molecule.
To highlight double-bond, let us first change the color of carbon atoms of the double-bond.
Click on Select atoms icon in the tool bar.
Then click on the carbon atoms involved in the double-bond.
A yellow halo appears around the atoms.
Open the Pop-up-menu.
Scroll down to Color, select Atoms and click on Orange option.
Now click on “Rotate molecule” option in the tool bar.
The double-bond in the cholesterol model is now in orange color.
Similarly, we can highlight the carbons in the side-chain.
Using Pop-up-menu, change the color to violet.
On the panel, we have a model of Cholesterol with important features highlighted.
As an assignment-
Load structure of caffeine from Pubchem database.
Highlight the important features in the molecule.
Modify the display to wireframe.
Now I will discuss another important feature of Jmol.
We can convert 2D structures of molecules, drawn in another software, into 3D models.
Here, I have a model of amino acid Alanine on the panel.
2D structure of this molecule was drawn in a software called GChemPaint.
The structure was saved as a ".mol" file.
GchemPaint is an Open source software for drawing 2D chemical structures.
Tutorials on GChemPaint are available at the following link.
To draw structures and save in ".mol" format, refer to Analysis of Compounds tutorial.
Shown on this Gchempaint display area are 2D drawings of-
Amino acid -Alanine
Nuclioside -Adenosine and
Saccharide -Alpha-D glucopyranose.
I have saved them in '.mol' format on my Desktop.
First let's view the 2D structure of Alanine as 3D model, in Jmol Application.
So, I will open a new Jmol window.
Click on Open a file icon in the tool bar.
I will choose Desktop folder and click on Open. Choose the file 'Alanine.mol' and click on Open button.
A 3D model of Alanine opens on screen.
Open the modelkit menu and click on fix hydrogens and minimize option.
Hydrogens are added to the structure and the energy minimized.
As with any ".mol" file, we can change the display using menu bar and also Pop-up menu.
Here is the 3D model of Adenosine.mol in Jmol.
And this is a 3D model of Alpha-D-glucopyranose.mol in Jmol.
Let's summarize.
In this tutorial, we have learnt to:
Load chemical structures from Pubchem data base.
Modify the display of Phenol and Cholesterol.
Convert 2D structures drawn in GChemPaint to 3D models in Jmol.
Convert 2D structures of Alanine, Adenosine and Alpha-D-glucopyranose to 3D models.
Here is another assignment for you.
Draw 2D structures of the following Amino acids in GChemPaint-
Cysteine
Histidine Phenylalanine
Save as '.mol' files.
Open the files in Jmol and modify the display.
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