Command Line Problem

[Johnny]

I ran arpeggio as so

python arpeggio.py my.pdb -s /D// -wh

python show_contacts.py my.pdb -s

So I compared my .pml file with the .pse file I got from the web server, and they're slightly different.

I would like to know how can you produce the same results that you get from the web server using command line? What are designated options for arpeggio.py when running on the web server? How do you produce .pse file with command line?

Thank you.