![]() ![]() The right to scroll through the text of this exhibit. you may need to do this several times, depending on the script. If you get an unresponsive script, please choose continue. This is especially true now that we are using JSmol and HTML5 instead of the java-based Jmol. Note: surfaces require a lot of memory and are slow to load. This helps with funding opportunitiesįor the OMM and helps ensure continued development of this resource. ![]() And pleaseĭrop an email to a link to your page/s. ![]() URL, Author,Īnd, ideally, a link to this page). Please explicitly acknowledge this in your work (e.g. Click on each command in succession.If this tutorial is helpful in the creation of your own webpages, When inititially loaded, the pyruvate kinase is rendered as green, vander Waals spheres, so that you can observe the effect of each command. Now execute tha commands descrbed in the figure above.īelow is an embedded Jmol image of pyruvate kinase ( 1liu.pdb) which you can use to interactively execute each of these commands. This will allow you to see the effects of the commands described in the figure above.Open the Rasmol Scripts console window and execute the following commands:.If you need help with this go back to " Creating Models". Relaunch Jmol and load the structure for pyruvate kinase ( 1liu.pdb).Clicking on each of the commands in the image below will take you to the corresponding entry for that command in the Jmol help file. Color the atoms in this selection according to their atom type.īelow are the corresponding commands you should type at the command line in the Jmol Rasmol Script console of the standalone version of Jmol.Render the bonds that connect the atoms in the selection by sticks that are 0.15 Angstroms wide.Render the atoms in this selection as spheres that have radii that are 20% of their vander Waals radii.Center the selection in the image screen.Restrict the selection to residue number 67 in chain A of pyruvate kinase, which is an aspartyl residue.This is the same structure that you opened with Jmol back on the " Before you get started" page. Koltun), who in the 1960's first developed models that used colors to identify atoms.To recreate the Ball & Stick model that is shown above, using the 1liu.pdb structure for pyruvate kinase, requires the following steps. The "cpk" has historical meaning and stands for Corey-Pauling-Kulton (Robert Corey, Linus Pauling and W.L. To color a model by atom type you use the command "color cpk". The "color" command has no default argument. In all to the models used so far, the atoms and bonds were colored by atom type carbons=grey, oxygen=red, and nitrogen=blue. The default for the "wireframe" command is to use sticks that are 1 pixel wide: The default for the "spacefill" command is to use the vander Waals radius: If not argument is provided a default value is used. Commands often have arguments which determine how the rendering is done. The commands that are used to produce this model are "spacefill" for atoms and "wireframe" for bonds. Below is a "Ball & Stick" model for and aspartic acid residue in the protein pyruvate kinase. When Jmol first opens a structure file it uses a "Ball & Stick" rendering of a molecule. Atoms and bonds can also be colored in different ways to illustrate various properties. Typically, atoms are rendered as, or represented by, spheres while bonds are rendered as sticks. For example, there are commands to produce various geometric shapes that represent atoms and bonds. Jmol contains a number of commands that can be used to display and highlight molecular models. ![]()
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