Olaf University is an exhaustive list of Jmol commands. The Interactive Script Documentation from St. There are many more Jmol commands than the ones covered here. subset strucno=19 select all cartoon on color orange.select all cartoon off wireframe off spacefill off.Type or copy the commands below into the console. Let's select, subset, and display a single alpha helix. The select strucno=X command will select entire secondary structural elements, such as α-helices and β-sheets. To see a list of structural elements to which selected atoms belong, type the show structure command in the Console after selecting some atoms. select resno=36 wireframe 70 spacefill 100 color cpk color cartoon red (display residue 36 on both chains A and B)Īnd see if you can spot the revealed amino acid residues! Many PDB files contain additional information about the secondary structures present in proteins.Logic operators can also be used to chain together resno selectors, or in combination with other kinds of selectors. ![]() Again, hovering over any atom in an amino acid will reveal its position in the amino acid sequence. This can be done using the select resno=X command. When dealing with proteins, selecting specific amino acid residues is often desirable. To determine atom numbers, click on the Jmol window and hover over the atom of interest. select atomno=X or atomno=Y, for instance, selects atoms X and Y. Set-logic operators like and, or, and not can be used to specify multiple atoms. To select a few atoms, use select atomno=X. Think about what kind of object you'd like to select when deciding on what selector to use. Selecting an atom or group of atoms is almost always the first step in entering Jmol commands. select (chain=B) color lightgreen (color chain A light green).select (chain=A) color lightblue (color chain A light blue).select protein cartoon only (turn on "cartoon" display mode).hide waters (hide water molecules in the structure).Either copy and paste or type the following commands into the Console: Open the Jmol Console by typing console on in the command box below the window. Applying a set of basic commands illustrates the secondary structure of the protein well. Now, try entering some commands on your own! The Jmol window at right shows the structure of an HIV reverse transcriptase. always visible as double sticks.Last Command: Part 2. (f) not fully implemented starting Jmol 11.7.32 only partial12 is implementedīy default, Jmol displays double bonds as twin sticks (cylinders) contained in the viewer's plane, i.e. (d) type 8 is defined as "any" in MOL format most versions of Jmol will render that as partial. ![]() (b) "partialDouble" and "aromatic" are identical except for which side of the bond is represented by a dashed line. (a) "hBond" and "partial" are both dashed, but they have different patterns, and newly created hydrogen bonds are only thin lines (wireframe style). bondOrder (new in Jmol 11.3.x) accepts a parameter specifying bond type (see table below). ![]()
0 Comments
Leave a Reply. |