You may also have to change the sigma contour level. When loading a
cryo-EM map, we have encountered that
COOT defaults to some very high sigma level, so that nothing is shown.
On 26/9/18 12:14, Paul Emsley wrote:
On 26/09/2018 03:59, Yangqi Gu wrote:
I am just beginning to learn Coot and model building. I have a very
basic question to ask. I used Phenix to convert my EM map into mtz
file using map_to_structure command, with h_min=3.4 A. And I tried to
examine it in Coot. However, no matter what I did, I could not see
the density of the mtz file. ( I tried zoom-in and zoom-out, change
the map radius). I also tried to open the original mrc file, I was
able to see my density. I am just wondering what I could do to
visualize my map?
It is not clear to me what is going wrong. I don't know about
map_to_structure and what it produces - if it works like refmac does,
it should produce an almost exact replica of the input map, so it is
strange that if you can see the map that you can't see the map from
the structure factors. Check the map histograms in Map Properties.
Do they match?
Paul.
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