On 19 May 2010, at 00:36, Paul Emsley wrote:
> Jay Pan wrote:
>> Hello Everyone,
>>
>> I have a reasonably well fitted electron density map through molecular replacement. However, there is always some red region left no matter how hard I tried when the mtz file is loaded into Coot. Is this because my model is still not good enough or it’s natural to most model fittings. In another word, should I be worried about the red region? Thanks in advance.
>
> Turn up the contour level and make it go away - that's what I do :)
>
> 3 or 3.5 sigma peaks are typical. Metals, carboxyls and disulfides are often associated with relatively strong negative density, some people try adjust their model to compensate (and others not, of course). As a rule of thumb, if you have 5 sigma peaks at the end of your refinement, that might be worrying/interesting.
The median height of the tallest positive peak after autoBUSTER re-refinement for the PDB *depositions* during April this year is about 7.2, and of the tallest negative peak about -5.0.
25/50/75th quantiles:
negative peaks -5.9 / -5.0 / -5.6
positive peaks 6.1 / 7.2 / 8.6
Tom Womack (Global Phasing)
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