Li Yang wrote:

> I have another question about loading a file using the script.  It used
> to be 
>  load 1ubi.pbd 
> will load the pdb file from current directory.  But now Jmol seemed to
> add the path of the directory where the application starts to the file
> name and it can not find the file even it is in current directory. Is
> this intended behavior?

In my experience, the default directory with the app is always the 
folder from which you open the app. It's not easy to set a folder 
from the console unless the Jmol.jar application and the files are 
together.
I guess that's a Java behaviour.
There is some environment variable that sets the "home" directory for 
Jmol. You may find that as a solution.
For me, the easiest is to put a copy of Jmol.jar wherever I want to 
work with model files, or use a testing webpage with the applet.






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