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I'm a little unclear on what you mean by "if i run the sony with calibre software".
Do you want to know if you can use the Sony Library software at the same time as calibre? That's a bad idea, because if the two of them try to update the PRS at once, they'll do Bad Things(tm) to its database.
On the other hand, there's no problem using them both so long as they're not running at the same time. A lot of us do that, though I personally haven't used Sony's weak software much if at all since I got calibre, as I refuse on moral grounds to buy DRM'd books.
If I totally misunderstood your question, please clarify.
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