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Jmol reference sheet1/29/2024 There are two main ways to determine what the unique identifier is for any given small molecule in a structure: To select and display these three zinc atoms: Every small molecule in a structure file is given a unique two or three-letter identifier that can be used to select them through the Jmol console.įor example, the 1zaa.pdb zinc finger structure has three zinc atoms, each with the two-letter identifier zn. These small molecules are often included in molecular structure files and can be selected and displayed in Jmol. Many proteins interact with small molecules that are not part of the protein chains. This is aesthetically distracting, and therefore should be avoided unless there is a specific reason you would like to display the backbone atoms. This means that the backbone atoms of the amino acid would be displayed, and partially show through the alpha carbon backbone display. If you were to add your sidechain without using the and sidechain syntax when selecting, it would produce a bumpy backbone. Watch This Command Demonstrated A "Bumpy" Backbone ![]() To add a sidechain for Histidine 29 in the 1zaa.pdb zinc finger protein: We also recommend using color cpk to color your sidechain by atom type. We recommend giving sidechains a spacefill of 1.25, which is large enough to hold them together and make them sturdy if 3D printed, but small enough to keep them from overwhelming the other features of your model design. To select and display a specific sidechain, you will use the select command followed by the amino acid residue number and end with and sidechain. All of the other atoms within the amino acid are not displayed, including the Sidechain, also called the R-Group.īut sometimes you may wish to display a specific amino acid residue's sidechain because it is important to telling the story of your protein, such as a sidechain that binds to a substrate or holds the protein together, even if the rest of your protein structure remains represented in backbone format. ![]() In backbone format, only the position of the alpha carbon in each amino acid is shown, representing a bend or kink in the backbone. ![]() Most protein models designed with the CBM's Jmol User Design Environment for 3D Printing use Backbone Format. Because of this, the specific amino acids in a protein are very important and directly relate to the protein's structure (shape) and function (job). Proteins are long linear sequences of linked amino acids that fold up into complex 3-dimensional shapes based on the order of their amino acids.
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