Hello Stanley 

The state saves information about the molecule, not the window.

Usually, the window size of the Jmol application is remembered, but that is in 
the hands of the operating system.

If you are in Windows, try to locate the users folder (in C) and inside your 
user there will be a folder named ".jmol". The file "history" saves the last 
used dimensions and position. Sometimes this does not work well, try 
deleting that file and then opening Jmol to see if it is reset.

Apart from that, yes, you can set the window size from the command line
See http://wiki.jmol.org/index.php/Jmol_Application#Interface




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