<p>+1 to what Michael just said with a couple of caveats.<br>
Firstly, of course, manual focus refers to focusing using the 'ground' glass not the electronic manual aid since that uses the AF system.<br>
Secondly, by adjusting the mirror it should be possible to get the centre focus point working OK but that does not ensure that the outer focus points are OK. Thom Hogan writes that there are lookup tables within the camera that ensure that the outer focus points work OK. This is presumably necessary since there is no easy way to ensure that the AF sensor is (optically) parallel to the image sensor and the tables correct for this though there is no way for a user to modify them. This means, therefore, that it might be possible to get the centre focus point correct but that the others will be wrong. It was apparently errors in the tables which resulted in the focus issues on some of the D800s.</p>
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