Next click 'Page Setup'. If you didnt select your device during the welcome wizard, you can set it here. The input and output profiles provide specialized optimization for your specified device. Be aware that not all formats are affected by the profile.
Thats it for the basic conversion options. Every option in the conversion dialog has a description of what it does which is displayed when you hover the mouse cursor over it. Look though the options and play with them to produce output that suits your taste. Options set in the conversion dialog are saved on a per book basis. Each time you click convert for a particular book, the options from the last time you converted it will be remembered. However, your changes will not be applied to other books in your library.
Clicking 'OK' closes the dialog and begins the conversion job. Look at the bottom right of the screen at the Jobs indicator. When it spins that means Calibre is working. Clicking it will show what job is being worked on.
When the conversion is finished the jobs count will drop by one. When the job count drops to zero the indicator will stop spinning. After the conversion is finished click the downward facing arrow to the right of the 'Send to device' button. Select one of the 'Send specific format' options (main memory is usually the best choice). A dialog will appear asking you which format you want to send. Select the format you chose in the conversion options. This allows you to specify what format you want sent to your device. If you don't explicitly select a format and you just click the 'Send to device' button it will send the 'preferred' format based on an internal format preference list which is device specific.
2.5: Limitations of conversion
Converting between e-book formats does have some limitations. One limitation of using a tool like Calibre is the inability to edit the e-book content before conversion. Calibre simply moves the existing content and layout from one format to another. Calibre is not a editing tool. If there are typos you wish to correct or layout changes you'd like to make, you will need to use a dedicated editing tool such as Sigil or Book Designer.
Another issue that often arises during conversion is missing or incomplete formatting. Not all e-book formats support the same formatting, so layout details may be lost when converting from one format to another. Formatting attributes, like bold and italics, will be preserved in most cases but complex page layout may not be. MOBI and EPUB both support complex formatting, so you wont have to worry about this as much when using these formats. However, MOBI does
not support all formatting supported by EPUB. Margins and fonts are two notable exceptions.
Finally, conversion will only shift what the input provides into another format. It will not add anything that was not already in the input to the output. If the input is poorly formatted, the output will be too.
There are some conversion options, Search & Replace and Heuristic processing that allow for some modification of the book's content. These options should be used with care. Since they modify the book's content there is the possibility of losing something by accident. It's best to avoid these options unless you know what you're doing.
2.6: PDBs: they are not all created equal
This is of particular importance to 1st generation Nook owners. Barnes & Noble sells e-books in both the EPUB and PDB formats and both formats are supported by the Nook.
PDB is not really an e-book format. It is a container for e-book formats. Think of it like a zip file. You put other files into a zip file so you only have to worry about having one file instead of many. That is essentially what PDB does for e-books. There are 28 e-book formats that can be put into the PDB container that I'm currently aware of.
An e-book reader, like the Nook, which supports PDB does not support all the possible formats that may be within a PDB file. The two most common formats found in PDB files are PalmDoc (also known as textread and Aportis) and eReader. PalmDoc does not support any formatting or images. eReader supports basic formatting and 8-bit images. The PDB files sold by Barnes & Noble are in the eReader format.
If you're converting to the PDB format for use on the Nook be sure to go into the PDB Output options and set the format to eReader. Otherwise the conversion will come out missing things like images and pretty much all formatting.
2.7: DRM: the bane of conversion
DRM is an acronym for Digital Rights Management. What is DRM and why is it necessary?
Lets think about physical books for a moment. With a physical book, you can lend or resell your book. But when you do either, you are without the book. With e-books, that is not necessarily the case. E-books are just files on the computer and they can be copied any number of times and given away any number of times. DRM was designed to prevent unlimited copying of an electronic file. Some e-book reader users would also note that it is a handy way for companies to try to lock them into a specific brand.