They are indeed in the direct map. Yes, you are right, hydrogen atoms are more readily seen in a cryo-EM
reconstruction than a map from x-ray data (given the same resolution of the data). "Atomic resolution" of
course doesn't refer the the data resolution required to resolve a hydrogen atom and the atom to which it is
bonded.
On 05/11/2020 09:11, Tim Gruene wrote:
Do you know why the hydrogen atoms only show up in the difference map,
but not in the direct map?
They are indeed in the direct map.
The signal strength of hydrogens relative to
C, N, O is quite strong, much stronger than for X-rays.
Yes, you are right, hydrogen atoms are more readily seen in a cryo-EM reconstruction than a map from x-ray
data (given the same resolution of the data).
The large blobs
that you illustrate in the difference map just disappear in the direct
map. Is this expected? After the hydrogens are modelled, they seem to
totally disappear...
This sounds like you've done some refinement of this dataset yourself. Is that
what you mean?
EMD-11638/7a4m.
Paul.
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