![]() By default, size is the last size used or else 500x500. Jmol.jar -geometry WIDTHxHEIGHT using lowercase 'x' and no spaces, e.g. To set the application's window size, use either of these:.File names and commands may need to be enclosed in quotes when they are not simple (it is safe to always use quotes). the commands written after lowercase "-j"Įither of the 4 may be omitted.the commands inside the scriptFileName text file (file extension is irrelevant, but we like to use. ![]() the commands written after uppercase "-J".Jmol.jar fileName -J scriptCommands -s scriptFileName -j scriptCommands irrespective of their actual order in the command line, they will always be run in this order: You can combine loading a molecular file, running a script file and running script commands (only Jmol 11.7.x and later):.To run a script file immediately after opening Jmol, use:.To load a molecular file immediately after opening Jmol, use:.Java -jar Jmol.jar -help Loading files and running scripts To show help for command-line options, use either of these:.Provided you have in the same folder/directory the batch file or shell script adequate for your OS (included with Jmol distribution). Otherwise, the general syntax for all cases isīut the 'java -jar' part will be omitted for simplicity (except where it is unavoidable). If you want to attach a Jmol icon to your preferred method of opening Jmol, you can get one from the Recycling Corner. If you have trouble running the application, see also Troubleshooting. Double-click on a molecular coordinates file whose extension has been previously associated to Jmol ( HowTo).From the command line: java -jar Jmol.jar (of course, issued from the folder/directory where Jmol.jar is, or else pointing to it with a full path).Execute one of the batch files/shell scripts that are part of Jmol distribution (Windows, MacOS, Linux, Unix).Click on a previously created Start menu entry (Windows terminology - HowTo).Click on a previously created shortcut (Windows terminology - HowTo).To open the application, follow these instructions: See also specific tips in Support/Linux, Support/OS X, Support/Windows, for example how to create a Mac OSX native installer. zip or tar.gz format) and extract/uncompress only the Jmol.jar file to the folder of your choice.
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