Hi Vivi
In principle, you include the path together with the filename:
jmolApplet(350,"load /whatever/path/is_your_file/S_0003_8934_0001.pdb");
However, using absolute paths is delicate, due to Java security restrictions.
That will only work from web server, not from local file.
Make sure to read a summary at
http://jmol.sourceforge.net/jslibrary/index.en.html#General%20Recommendations
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