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.
