Dear community,
As far as I understand, negative density features point at stuff that is in the model, but not supported by experimental data.
However, in many cases (e.g. attached image), when you visualize the densities, there are negative (red) density blobs not containing any atoms inside. Just empty space inside. There is nothing in the model in those regions of space. How it should be interpreted?
Could you tell me please what I am missing?
Would be grateful for any help,
Best wishes,
Aliaksei
Even in a well-refined structure some residual difference density is always expected. In this case the small negative peak could have to do with imperfect bulk solvent modelling/scaling. I wouldn't worry about it too much, it's very minor in this case. The negative difference density at the carboxylic acid group of the glutamate however could be indicative of radiation damage; in that case refining with lower occupancy can be a solution. Other tell-tale signals for radiation damage are e.g. cleaved Cys-Cys disulfid bonds. HTH, Jonathan.
In layman's language, negative density is nothing but the regions where you build nothing, protein backbone or heteroatoms or anything because probability of finding atoms in these regions is zero so one should not build anything in red/negative density.
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