There's a 64-bit linux GUI which I compiled in Nathan's
SoPDF Frontend thread. It looks like no one ever got around to compiling a 32 bit linux version. You could do it yourself following Nathan's advice there. You could then share it with the community.
If you don't have time, or are too intimidated (which would be understandable; Nathan's instructions are not as clear as they could be...), I'm hoping to get around to doing this myself. I don't have a 32 bit linux system running right now, but I've been thinking about trying Lubuntu on my Notebook, which is only available 32 bit if I'm not mistaken. I was going to wait until the semi-official Lucid version is out, which I think should be in the next few days (Ubuntu/Kubuntu were released today, as you know.) If I end up doing that, I'll be happy to compile the GUI, but you'll have to give me a week or so.
Once you figure out what your favorite options are, it would also be trivial to write a bash script which you could call with from within the right-click context menu when browsing folders in nautilus. I do that on my machine. I'd be happy to share mine if you tell me what your favorites are.
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For some pages, the last line (or last two lines) are not so crisp (a little faded I would say). I do not know to what attribute this -small- display defect.
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This is just a hunch, but I suspect this has nothing to do with soPDF. The Sony Reader, or at least the 505, when viewing a PDF in landscape mode, so that you only see half the page at once, will fade out the edge bordering the other half of the page. It's its way of reminding you that there's more to see.
Personally, I find it very annoying.
Actually, one great way around this is to use the "Fit2xWidth" (or -m0) option in soPDF, which will, in addition to cropping, splits the pages in half and rotates them 90 degrees. That way, when you load them on the Sony, it'll look just like it does in landscape mode when the device is still in portrait mode, so you won't get this faded areas. (You'll also get portrait menus, which I prefer to the landscape ones, because the numbers line up with the number buttons...)