On May 18, 2010, at 4:13 PM, 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.
Negative density (with absolute value above 2 sigma) sitting on atoms
is much more of a concern than random negative peaks floating in the
solvent breeze, as it indicates misplacement of the model.
> In another word, should I be worried about the red region? Thanks in
> advance.
I've alway found it very helpful to worry about absolutely everything
obsessively to the point where it causes endoderm to bleed. Which is
why, I suppose, Paul chose red.
>
> Jay
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