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The can be hidden and displayed by clicking on the in the upper left corner of the JSmol viewer.
The toolbar strives to give you control over JSmol while remaining intuitive and user-friendly. Let's begin at the top.
First, set the of JSmol.
Next, adjust the .
Turning on will render a smoother model, but it comes at the cost of slower animation speed.
The is automatically set by JSmol depending on the speed of your device, but you may find it beneficial to lower the setting while looking at large models or complex animations. Certain features (such as surface models) will be removed at lower platform speeds. Try lowering the setting to "Maximum Speed".
The button lets you set a custom spin in JSmol by dragging and releasing the molecule. The molecule will continue to spin with the direction and magnitude it was released with. You can disable this feature by unchecking the option.
The background color and performance settings will be remembered until you close your browser window. All other options will be reset when you navigate to a new page.
The buttons found in the field allow you to easily toggle , , and on and off.
Many default settings will force features on or off. Specific labels are often paired with each article in order to simplify the display and aid with learning. However some articles may be without a unique label, in which case the label button will turn on a default label based on the type of molecule displayed.
Take the current model as an example. labels on. Ribosomal Protein L11 contains both RNA and protein. Instead of labeling every atom, the default label only labels the lead atom (alpha carbon for amino acids, phosphorous for nucleic acids) of each residue. The syntax is [residue]-[position]:[chain] and the label text is colored by the "amino" and "shapely" JSmol color schemes.
From the toolbar, you can atom sets from a series of menus. More detailed descriptions of the selections are available if you hover the cursor over the item of interest. Selected atoms are displayed with a yellow "halo".
will select every atom in the current file. This includes atoms that are hidden.
The allow you to create custom selection sets. Checking or unchecking the will add or remove the corresponding parameter from the selection set. For example:
Select all .
Narrow the selection by adding .
Further isolate the selection by including .
The result is all carbons that are found within the nitrogenous bases of the nucleic acid.
It is possible to create non-logical selection sets; for example, selecting {Carbon and Water} or {Alpha Carbons and Sidechain} will return nothing.
The will change the way that the selected atoms are modeled. Display options are split into "Atomic Models", which represent each atom individually, or "Structural Models", which simplify the atoms into a model of overall structure.
The are also separated into two categories: "Basic Colors" and "Color Schemes". The latter can be used to color atoms based on their properties.
The tell JSmol what to ignore and what to alter. For example, if the display option is checked, changing the selection will immediately write the current display option to the new selection. Use this to target your commands.
If no selection is made, a change to the display or color settings will be applied to every atom in the model.
Structural models omit some atoms from the display.
Using what we've learned so far, we can create a custom model to get around this problem. Try this:
Display as Mesh Ribbons
Color Structural Motifs
Select Sidechains
Display as Ball-and-Stick
Color Shapely
Uncheck selection or press to remove halos.
The atoms of the backbone are now generalized as ribbons and colored based on their secondary structural motif while the atoms of the sidechains are individually displayed and colored based on the amino color scheme. You may have noticed that the sidechains appear to float next to the ribbons. This is because in order to draw a bond between two atoms (e.g., the alpha- and beta- carbons), both atoms must be displayed as ball-and-stick or wireframe models. But if we change the lead atoms to one of these models, neither protein or nucleic acid will be displayed using the ribbon model, as lead atoms are part of the backbone that the ribbon model interprets.
The ability to visualize one atom using two models is a limitation of the toolbar. We will learn how to overcome this problem on the next page.
The toolbar is designed to let you explore your curiosities. It is entirely optional, and the content of the tutorials, written by Dr. David Fahrney, will guide you smoothly through the material. To hide the toolbar, simply click the . The site will remember your choice as you navigate between pages.
In addition to using JSmol, we recommend ICN3D ("I See In 3D") for further exploration of structures in 3D. ICN3D is linked to many standard databases, such as the Protein Database (PDB) and AlphaFold Protein Structure Database, and has loads of predefined selections and sequence annotations for ease of use. To compare and get started, check out the Ribosomal Protein L11 in ICN3D:
