5/16/2023 0 Comments Select chain command jmolWith select nucleic, all atoms that are part of nucleic acids (DNA, RNA) will be affected by future commands. With select sheet, all atoms that are part of beta pleated sheets will be affected by future commands. Note: Jmol does not recognize 'helices' (plural) but only 'helix' (singular). With select helix, all atoms that are part of alpha helices will be affected by future commands. With select hydrophobic, only the hydrophobic amino acids in a protein will be affected by future commands.Ĭolor yellow select hydrophobic color yellow To color this selection lemon chiffon, type:Ĭolor lemonchiffon select sidechain color lemonchiffon With select sidechain, only the atoms that are part of sidechains in a protein will be affected by future commands. However, if you are displaying the alpha carbon backbone, in which a line (backbone) connects adjacent alpha carbon atoms (colored cyan in the backbone here: N- C-C=O), you should use the following commands:Ĭolor backbone cyan select :a color backbone cyan The commands above will select all atoms in the peptide backbone - so the N-C-C=O atoms. Note that preset Jmol colors do not have a space between words in the command line. To color this selection dodger blue, type: With select backbone, only the backbone atoms will be affected by future commands. To do this, use the select all command followed by color gray. Note: The Jmol buttons of Top 7 shown below have been reset before each set of commands. You should get a feel for whether the number of atoms selected is what you expected. Note: When a select command is executed, Jmol displays the number of atoms selected in the Jmol Console Window. With select all, every atom contained in a PDB file is selected and will be affected by future commands. Select all is the default Jmol selection. (Following the select command, a second command is entered to color the selected portions of the molecule.) Select All Please click the button after each description to see how Top 7 from 1qys.pdb will look with the selected area colored red. To change another part of the molecule, you have to enter a new select command. The display will NOT change until you supply additional commands, and those commands will ONLY operate on the parts of the molecule you have selected. When using the select command, Jmol will respond with '# atoms selected', where # will be the number of atoms selected. Below is a description of commonly used Select commands along with a Jmol button. However, we can specify parts of a molecule that we want to display differently by using the Select command. Thusfar, every command we have typed into the Command Line has affected the entire protein. Please see Getting Started with Jmol for information on how to download and open PDB files. Which of the following sequences of Jmol commands is the best way, according to the jmol tutorial guide, to color the ends blue and red so that it can be printed on our 3D printer? O select all backbone 1.5 select 1 color blue select 45 color red calculate struts struts 1.0 color struts black O select all wireframe off spacefill off cartoon off backbone 1.0 select 1 color blue select 45 color red calculate struts, select struts color black O select all wireframe off spacefill off cartoon off backbone 1.5 color 1 blue color 45 red calculate struts struts 1.0 color struts black O select all wireframe off spacefill off cartoon off backbone 1.5 spacefill 1.25 wireframe 1.0 color 1 blue color 45 red calculate struts, struts 1.0 color struts black O wireframe off spacefill off cartoon off backbone 1.5 select 1 color blue select 45 color red select all calculate struts struts 1.0 color struts black Q5.Unless otherwise indicated, this section of the Training Guide uses the protein Top 7 based on PDB file 1qys.pdb. You click on "get pdb" and load a 45-amino acid protein. You have just opened Jmol 14.3.16 and the console.
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