Francois Berenger wrote:
When I run coot in order to read the experimental MTZ corresponding
to the PDB I am viewing, [snip]


I am afraid coot is refining my molecule instead of just displaying the map.

Well, Refmac is - at Coot's request.

This usually happens because Coot doesn't detect phases in your MTZ file (i.e. you are using a phasing input file, rather than an output file). Or it could be a bug.


Paul.

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