Thiago: if I get you right, it's a rather long way, at least conceptually, from diffraction images to atomic models. Essentially you want to compute the Fourier transform of your diffracted data, with the handicap that (from the downloaded images) you don't get the phases necessary to complete the Fourier transform process (this is why methods like Molecular replacement -your case?-, SAD, MAD, MIR ... are required to first get some phase information). I suggest you to read at least a crystallography primer; else, no software package will be that helpful. In any case, you may refer to the CCP4 suite, where almost every computational need, from data reduction to pahsing, refinement and graphics are offered.

Martino

Hi Thiago, I agree with Martino's suggestion that you must first read about X-ray crystallography. Literature on X-ray crystallography is vast. I would recommend you to read this article (http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2007.06178.x/full) and at least these two books: 1) Crystallography Made Crystal Clear by Gale Rhodes and 2) Biomolecular Crystallography by Bernhard Rupp.

Good luck!

Avinash 

This course is a good starting point for you

 http://www-structmed.cimr.cam.ac.uk/Course/Overview/Overview.html

Hi, I was looking at classes at youtube and reading some documents but I wasn't be able to clearly understand the steps.

Martino: Thanks a lot for the key words and the software CCP4, the sentence "data reduction to phasing" got me the right page to understand the steps using the CCP4.

Avinash: Thanks for the book suggestion I saw here some sample pages from the Bernhard's book and looks really good tool to learn, I'm going to get one.

Oluwatoyuin: Thanks for the course link, seems a good place to start for free.

In case somebody else came looking for the same thing, this is a link with the steps and the tutorial for each step using CCP4

http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Using_the_CCP4_software

Hi,

as people said: it is a long way. So if I may, i will advise you some reference book to start study the subject.

http://www.ruppweb.org/garland/default.htm