> You have to make .pml file and put the python commands inside pymol
> blocks.

it's "python" blocks, see:
http://pymolwiki.org/index.php/Python

> ... do I need to put those code in another .py file?

That's also possible, yes.

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

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