How is it possible to precisely map huge molecules? Somehow, scientists easily know the structure of a compound of any complexity.

What techniques are used to know the sturcture of molecules like this one, or complex proteins that can be constructed of thousands of atoms, like the ones used in intracellular processes? It is so common to see them drawn as structural formulaes or pictured in a video, with a fine per-atom precision... but how?


This update addresses the comments about the question being too broad.

Firstly, I want to say that for me this question is rather exact - here and there, in lots of places over the internet, I see structural formulas and 3D models of countless chemical compouds that claim to bear a 100%-precise depiction of the actual molecule structure (I have linked an example). And I am interested in how all this data is gathered and why is it 100%-correct? I am so used to the pictures of all these complex compounds that I take them for granted. But recently I became to wonder, how do we even get these, how this knowledge is received?

Secondly, although there's certainly a difference between a structural formula and a dynamic 3D model like in this video, it is not so important in this question. The fact that we can precisely depict any compound or molecule is not even in question, it looks like that there's no problem in doing so for any chemical.

The very exact question is: what is(are) the method(s) of getting such precise formulas and pictures for objects (molecules) that are not even visible to the naked eye or microscope?

Of course, there can be differences in how the mapping is done for different molecules, or some data, like the 3D model can be complemented by some computation conducted with help of a computer, but all in all, what is the basis of our confidence of being able to exactly know a structure of any molecule?

Though, especially, after reading the comments, I think that a proper answer could be too large and include historical data..

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    $\begingroup$ Your question is rather too broad in it's current form imo. Also are you asking about constitutional data (sequence) or conformational (3-D structure)? $\endgroup$ – Mithoron Nov 3 '15 at 1:41
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    $\begingroup$ I agree with @mith it's too broad now. There are many methods that can be used for structural elucidation, such as IR spectroscopy, NMR spectroscopy, X-ray crystallography, and mass spectrometry, not to mention a whole host of microscopy techniques. Often, it is a combination of these that are used to arrive at the correct structural formula. $\endgroup$ – orthocresol Nov 3 '15 at 9:01
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    $\begingroup$ Historically, before the technologies mentioned above were developed, chemists applied various degradation and derivatization reactions to produce relatively simple fragments that could be positively identified by their properties. By working backwards from these fragments to the original compound, one could infer its structure. Some of these historical structure elucidations remain among the classics of the chemical literature and illustrate the importance of logical thinking in chemistry. $\endgroup$ – iad22agp Nov 3 '15 at 14:43
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    $\begingroup$ We didn't really mean to say that the question was too unclear, or unspecific. It is actually a very good question (I mean it), but it is probably not too suitable for SE because any proper answer would be too long. There have been so many methods, used in the past and present, in order for chemists to actually find out what they were doing - as you see, the two comments directly above already listed multiple chemical and physical methods, but without even saying anything about what they are. So... it might be good to narrow the scope a little bit, or perhaps do some reading on your own. $\endgroup$ – orthocresol Nov 3 '15 at 16:17
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    $\begingroup$ Agreeing with @orthocresol there. There are a plethora of methods that one can use and historically has used. Some are still used today, some are not; some can do all the work by themself, some need assistance by others. Often, structures are drawn even though they are not truely proven just because it makes more chemical sense than anything else. It is nigh impossible to answer this properly unless one is very bored and has lots of time. $\endgroup$ – Jan Nov 3 '15 at 16:39