You will see the two structures superimposed with two mutation regions highlighted. Drag and drop this script into your Jmol script editor window and run it. displaying user-defined dipoles load water.xyz moveto 1.0 727 -680 95 37. A set of commands is called a command script, and writing such sets of commands or scripts is called scripting. This prototype page illustrates the new capabilities of Jmol to calculate and display dipoles and simple arrows. Keep in mind that you should have a vision of what you want to accomplish before consulting a scripting reference. Olaf University is an exhaustive list of Jmol commands. The Interactive Script Documentation from St. Jmol, a Java applet used to view molecules in web pages, can read scripts that are contained in Jmol buttons. Now we can use the script below to highlight the mutated regions. The script run in this case was water.xyz. The best way to think about using Jmol is to imagine what you would actually like to do, then figure out which scripting commands fit your purpose. Jmol still thinks the center of the entire model is the zoom center, so zooming flies right past the helix. Before you use the script below we need to activate both models in the Jmol viewer by right clicking and selecting "All 2 models" and ticking all. There are two structures in this file and to select each one separately the notation is 1.1 for the first and 1.2 for the second. JSmol is not a different program than Jmol: it is Jmol, just compiled into JavaScript instead of Java, and thus those who are familiar with scripting Jmol. Load the superimposed structures into Jmol (use open file). Note that the structural alignment is saved as two models in one PDB file, model 1 (4gw3) and model 2 (4hs9)
This shows the PDB formatted alignment file in a new window and then you can use your webrowser's save-as facility to save the file. Scroll to the bottom of the results page and select
JSmol2wp creates a button with the label. This gives the alignment results in a new webpage with an interactive Jsmol viewer for quick visualization.ĭownload the superimposed structures (in PDB format). Individual ommands have the format labelscript, where label is the text you want on the button, and script is the Jmol script you want to run.JSmol2wp parses these, first by splitting on the string and then on the character. Enter the PDB IDs of the 2 structures (make sure you enter them in the order First ID: 4gw3, Second ID: 4hs9 (as this influences how we can maniplulate the structures in Jmol using scripts later on).
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