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Originally Posted by ren41
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What would be the best way to put the file into Calibre for conversion?...
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Since MOBI is an HTML based format your best bet will be HTML or some HTML-esque format (e.g. ePub). As theducks said, you need to be very aware of what formatting is supported in MOBI and what isn't.
Personally, I prefer working either in HTML using Dreamweaver and/or Notepad++, using a browser for preview with the latter, or working in ePub using Sigil as the editor. Either of these two formats will be the closest you can get to MOBI in an editable format. I then do my conversions to MOBI in calibre.