4 - How to use Jmol

1 Now that the molecule is on the browser page, what can I do with it?

A looooot!!!

Jmol has a menu with several operations, hundreds of commands, and perhaps another hundred tutorials on the internet. For more direct and immediate structural observations, however, the operations can be summarized as follows:

• Mouse movements (rotation, translation, zoom)
• Model representations (ball and stick, filled space, wireframe)
• Colors (model and background)
• Measurements (distances and angles)
• Molecular characteristics (H bonds, van der Waals cloud, partial and effective charge)
• Surfaces (molecular, electrostatic)
• Atom selection and visualization (water, hydrogen)
• Animations (zoom, automatic rotation), cuts

2 Saving the model on your computer or mobile device

All actions performed on the molecule produce a new model that can be downloaded to your computer. This is really cool because the modified molecule (with changes in colors, representations, animations, for example) can be uploaded to Jmol or JSmol (internet) as already mentioned. To do this, you can use mouse clicks or command lines, as follows:

1. Right click on the screen -> File -> Save -> Save as PNG/JMOL # by mouse
or...
2. write molecule_name.pngj # by command line in the Console

One of the impressive features of Jmol is that by saving the molecule as PNG/JMOL, you can open the file as a static image with a double click to just show the molecule, or drag the file to the Jmol window in your browser, which will load the three-dimensional and interactive structure of the model!!!

Now it’s up to you:

1. Load a model for “phenol” by typing in the Console: load $phenol
2. Save the model by typing in the Console: `write phenol.pngj
3. Change the orientation of the model randomly with the mouse (just move it a little);
4. Locate the file phenol.pngj on your computer;
5. Open it as a normal image, just to test;
6. Now drag the file to the Jmol online window and see if the model replaces the previous one (just check the orientation)

2.1 Some movements in Jmol

To illustrate some actions, we will initially use the vitamin C model, loading it with the command below in the Console.

load $ascorbate

3 Mouse movements

For rotation and translation of the model, as well as magnification:

zoom - middle mouse button; if there is no middle button, Shift+left button; 

rotation - left mouse button

translation - Ctrl+right button

rotation on the axis - Shift+right button

4 Representations of the model

The representations refer to the visual aspect of the model (rendering), or its style. Thus, Jmol can render the model as stick, wireframe, filled space, ball and stick, trace, and cartoon (all in English, of course - cpk, wireframe, trace, cartoon).

Try these styles, including the only option. This option allows the action not to be superimposed on previous ones (in this case, the superimposition of representations). To do this, copy, paste, and execute on each separate line the code snippet that follows in the Jmol Console, whose rendering illustrates the fluoxetine molecule.

load $fluoxetine # loads the molecule
wireframe only # wireframe style
cpk only # filled space
cpk 20 only, bond 1 # balls and sticks
cartoon only # cartoon representation, but this does not occur with small molecules, only with biomacromolecules (proteins, nucleic acids, for example)

Note also that the cartoon representation does not result in a rendering for the fluoxetine model. This is because the cartoon representation is restricted to biopolymers only, i.e., proteins and nucleic acids, and some supramolecular associations.

However, if you want to try cartoon, you will need to know the alphanumeric code for a protein or nucleic acid. For example, for myoglobin, an oxygen-carrying protein in mammals (code: 1mcy)

load=1mcy # loading myoglobin

# Note: note that the command line for biopolymers is slightly different from that used for small molecules

Note that the default rendering for large molecules is balls and sticks, which is not very educational for learners. In this case, it can be represented as a unique drawing by typing:

cartoon only # rendering as a drawing

To obtain this and other protein and nucleic acid codes, enter the PDB - Protein Data Bank, RCSB database and type the name in the search field (in this case, myoglobin). The system returns several structural models and their codes. Simply transcribe one of these codes to the JSmol Console.

If you would like to learn more about biomolecules and the use of Jmol, I invite you to visit the Biochemistry portal.

5 Colors

There is great flexibility in colors for Jmol (and, consequently, for JSmol), both for entire models, parts of the model (specific atoms or a set), and the background. The default color display follows the [CPK (Corey–Pauling–Koltun)] convention (https://en.wikipedia.org/wiki/CPK_coloring). Using the previous vitamin C model (load $ascorbate) as an example, try the following variations separately:

color pink
color blue
color ligthgreen
background yellow # background color

The last command in the list above allows you to vary the background color.

Additionally, it is also possible to color the bonds between atoms, as follows:

color bonds LightSeaGreen

For a wide range of colors, you can consult the Jmol Colors reference, or a more “digestible” link, created by us while learning the program for higher education, in the Biochemistry area, more specifically, the topic on colors for Jmol.