Right-click on the sequence ID label of FER1_SPIOL to open theĬontext menu and select 3D Structure Data. file and have it opened in Jmol, by setting the default ("open") action of such file extensions, as described in the above sub-section.Viewing Structures with the integrated Jmol ViewerĬlose all windows and load the alignment at You can set a hyperlink for any object in MS-PowerPoint that points to a pdb, mol, etc. Linking from PowerPoint to molecule files so that they open in Jmol application "C:\Program files\Java\bin\javaw.exe" -jar "C:\Program files\Jmol\Jmol.jar" "%1" " put here the path and filename of javaw.exe " -jar " put here the path and filename of Jmol.jar " "%1" In the textbox under "Action" you can type "open" or whatever you want it to be called in the pop-up menu under "Application used" type (including the quotes and the final %1):.Click on "Advanced options" button and then either "Edit" the default "open" action or create a "New" action.Open windows explorer / file manager, open menu " Tools → Folder options", "File types" tab, and scroll to pdb (or any other extension that you want associated to Jmol, like mol, mol2 or xyz).Locate the file javaw.exe in the Java installation folder (usually it will be somewhere like C:\Program files\Java\bin\).Locate the application file, Jmol.jar (you decided where to put it when you uncompressed the downloaded Jmol distribution file, jmol-11.xx. or jmol-11.xx.xx-binary.zip).file (or right-clicking for options in the pop-up menu) will open it with Jmol application. You can configure Windows Explorer (file manager) so that double-clicking on a pdb file, or mol, xyz, etc. The same applies to entries in Windows Start menu, or Programs menu.Īssociating molecular files in hard disk with Jmol application Change Icon: you can get a Jmol icon from the Recycling Corner.If not specified, Jmol will ususally point to My documents, or Documents, or the Desktop. Start in: you can put your working folder, if you want that will be the default location Jmol will show on "File > Open"."C:\Program files\Jmol\Jmol.jar" -s "myScript.txt" "C:\Program files\Jmol\Jmol.jar" -J "set language pt_BR" java -Duser.language=pt_BR -jar "C:\Program files\Jmol\Jmol.jar" Another example: to start Jmol running an initial custom script (set of commands), prepare such script in a text file and use this: For example, to force the Jmol interface in a language different from the system's language, you may add either of these to the target textbox (example for Brazilian Portuguese): "C:\Program files\Java\jre1.8.0_251\bin\java" -jar "C:\Program files\Jmol\Jmol.jar" These last two syntaxes allow to add extra start-up specifications, between java and -jar, like the amount of memory to be used, the window size, or the execution of a script, etc. Java -jar "C:\Program files\Jmol\Jmol.jar" and if the system is not configured to locate the Java executable, you will need to indicate its full path, like e.g. "C:\Program files\Jmol\Jmol.jar" For more flexibility, you may instead wish to call Java explicitly using this: Target: the place where you have put Jmol files (usually when you uncompressed the distribution gz or zip file), including full pathname and filename and all between double quotes.Shortcut properties must be (under the Shortcut tab): What is given here are the specific details for Jmol. The details of creating a Windows shortcut and a Start menu entry are out of the scope of this wiki. The substitue for web pages is the JSmol object which runs without problems and provides the same functionality as the Jmol application. Running Applets inside a web page relies also on the Java virtual machine, but has been disabled in most web browsers. Jmol runs without problems on computers with Windows 95 or later, using Oracle's Java virtual machines, as an Application.
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