hello~do u know how PDB,mmCIF,PDBML/XML file formats being created?thanks!
The structural data in the files comes from experimental methods such as x-ray crystallography, and NMR or predictive techniques.
Other data in the files - publications etc. will be entered manually, though sofware tools may be used to do this, and they may aquire some information automatically from other sources.
There are many software programmes available to convert between the file types you mentioned - many bioinformaticians will write their own software based on open source libraries such as http://www.bioperl.org, the context sensitive adverts below often carry commercial applications for producing these files.
If you have obtained the free PDB viewer Deep View http://www.expasy.org/spdbv/ you will see that it has an ability to edit as well as simply view structural data files.
If your question was directed more at how the structural data is obtained in the first place, I suggest either one of the books recommended:http://www.scientistsolutions.com/index.php?a=topic&t=605
Or http://en.wikipedia.org/wiki/Protein_structure and the links in that article.