This Jmol Exploration was created using the Jmol Exploration Webpage Creator from the MSOE Center for BioMolecular Modeling.
This section of the Training Guide uses the protein Top 7 based on PDB file 1qys.pdb. Please see Getting Started with Jmol for information on how to download and open PDB files.
You may wish to display specific amino acids that are important in your protein, such as those that bind a substrate or other ligand. If the interaction involves sidechain atoms, your model will be less cluttered and more aesthetically pleasing if you don't display the backbone atoms.
In this section, we'll use Boolean operators to select just the atoms in the sidechain and display only these atoms. Please see Select Command and Boolean Operators if you need more information about the select command or Boolean operators in Jmol.
To select and display only the atoms of the sidechain of a specific amino acid, you want to use the select sidechain command followed by the amino acid name/number and end with the and (sidechain or alpha) text.
select lys58 and (sidechain or alpha)
or the shortcut in which a comma replaces 'or'
select lys58 and (sidechain, alpha)
This command selects the lysine at residue 58, but limits the selected atoms to the sidechain atoms and the alpha carbon of that amino acid. Note that a comma can be used instead of 'or' in Jmol.
Note: It is important to select the alpha carbon atom in addition to the sidechain atoms because this will attach the sidechain atoms to the alpha carbon. Without the alpha carbon, the sidechain will build as a separate unit from the rest of the protein.
Once your sidechain is connected, give it wireframe and spacefill dimensions:
Click the button below to see the lys58 sidechain displayed on Top 7.select lys58 and (sidechain or alpha)
Note: These two commands together will generate a ball and stick appearance. You can enter just the wireframe command and create a 'sticks' appearance. If you enter just the spacefill command, the atoms will be displayed as little spheres and the spheres may not be securely connected to one another. The image MAY look fine on the screen, but the model will come out of the 3D printer in pieces that can't be put back together! It is therefore imperative to add the wireframe command to connect the spheres together.
If you do not use the and (sidechain or alpha) command when displaying sidechains, you will generate a 'bumpy backbone'. The amino nitrogen and carbonyl oxygen backbone atoms protrude from the smooth alpha carbon backbone. Unless the backbone atoms of the amino acid play a specific role in the story you are telling (see the next section of this tutorial), you'll want to avoid a bumpy backbone.
Click the button below to see an example of a 'bumpy backbone'. Here, the command select lys58 was used instead of select lys58 and (sidechain or alpha).select lys58
When we left out and (sidechain or alpha) in the select command, it produced a bumpy backbone. If you discover that you have a number of sidechains displayed with bumpy backbone, you can use this quick fix:
Note that this quick fix should be used cautiously. If you are deliberately displaying backbone atoms (see next section), the commands above will also remove any displayed backbone atoms. These atoms would need to be added in again.
If you have a bumpy backbone for a single residue (let's say lys58), you can correct the problem with the following commands:
select lys58 and (sidechain or alpha)
Occasionally you'll want to display a backbone atom that is important to your protein's molecular story. In this case, it is acceptable to show the corresponding backbone atom(s) that interact with the ligand.
First, identify the atom number of the particular backbone atom you want to display. You can do this by selecting the entire amino acid and displaying all of the atoms in spacefill.
Note that we use a spacefill size LARGER than the backbone size. This is so we can see all of the backbone atoms. Let's assume that we want to display the blue backbone nitrogen atom. Next, click on the atom you want to display; the atom number will be displayed in the Jmol Console. Now, turn the spacefill off on the whole amino acid.
Lastly, select only the atom number of the backbone atom you want to display and turn spacefill on. There are two alternate versions of these commands:
or the shortcut:
Note: The spacefill command uses a larger value than normal so that the atom will protrude from the backbone. You may adjust the spacefill value from 1.25 to 1.6 to determine the size that best displays the backbone atom.