With the key subset in place, we can now think separately about the ligand and the protein. Load it up later by pasting the text into the Console. If you're worried about messing up your structure while executing a command, use the write state command to save your work! Copy the output of write state to a text file to save the appearance of your Jmol. We can restore the default selecting behavior by subsetting the entire structure (avoid doing this for now).īe careful! Jmol commands are irreversible. Notice that only the bonds in our subset are altered, even though the select command we used was "select all"! With the subset confirmed, let's widen the bonds again. For visual conformation, let's select the subset and make bonds thinner. To simplify future commands, let's subset the currently displayed atoms so that no commands extend beyond the scope of these atoms. Hover your mouse over an atom to see its atom number and what built-in atom group it belongs to (a three-letter abbreviation in brackets).įrom here on out we would only like to work with this atom set. Can you see what we've done? Only the DR7 inhibitor and two amino acid residues are now displayed in the Jmol window. To zoom in on the display, Shift-click and drag on the Jmol window. After reading a reference and exploring the 2FXD structure on the Protein Data Bank, let's imagine we learned that the ligand exhibits two hydrogen bonds with two aspartic acid side chains on the protein.įirst, let's select and hide the entire structure, then select and display only what we need. The Jmol at right is a complex of an HIV reverse transcriptase with an inhibitor-but you wouldn't know it from the view shown! Let's clean this structure up to highlight the role of the ligand and how it interacts with the protein. To do this, you will often have to "whittle" structures down to their essential components. We would like you to distill the behavior and properties of macromolecular assemblies to the level of "bonds and atoms" we explore in CHEM 332. Note that its action is not cumulative, but exclusive.Last Command: Part 1. Reversibly removes part of the molecule from view (without changing the assigned rendering style). Sets the diameter of the sphere representing an atom (most usually in percent, relative to Van der Waals radius)Ī schematic rendering that is relevant only to protein and nucleic acid chains. Sets the thickness of a stick representing a bond (in angstroms needs a decimal point). color chain color each macromolecule chain in one color (good to find out the nr.color group color macromolecules by the order of residue in the chain.color structure color proteins by type of secondary structure.Select within(2.8, ) all atoms at 2.8 angstroms or shorter distance from any atom that belongs to the group(s) named "ATG"Īpplies a color to the selected atoms, their bonds and other graphic elements attached to them. Select within(3.0, atomNo=87) all atoms at 3 angstroms or shorter distance from atom number 87 Select within( group, atomNo=87) all atoms in the same group as atom number 87 Select within( group, _Mg) all atoms in the same group as a magnesium atom It has several variants or uses among them: Most frequently employed as part of a select command. select 33,36,37 residue numbers in a chain.selectĪn essential command, as any style of rendering that you want will apply only to the set of atoms that is selected at that moment. For example, monoatomic ions (Ca 2+) are part of the ligand set, while isolated nucleotides like GMP will be identified as nucleic and hence not ligand. are not part of a protein or a nucleic acidīe cautious it will not always select what you may think are "ligands".This is also a keyword for an atom expression. It refers to the set of atoms identified by Jmol to be part of a protein (due to their chemical structure containing the key atom names). This is not a command, but a keyword for an "atom expression". Jmol Commands Some relevant Jmol commandsĪ very basic introduction for full details, see the Jmol Scripting Documentation.
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