[phenixbb] mrc to mtz conversion to open map in coot

Paul Emsley pemsley at mrc-lmb.cam.ac.uk
Wed Aug 2 11:57:20 PDT 2017

On 02/08/17 19:49, Joshua Jude Lobo wrote:
> Hi phenixbb
> I am new to phenix and am trying to convert a cryo-em map(mrc format) 
> to mtz format using the phenix.map_to_structure_factors command .This 
> proceess finishes without errors but the resultant mtz file is not 
> viewable in coot . I have tried both the phenix.map_to_model and 
> the phenix.map_to_model_histogram_1.12-2829
> How is the best way to troubleshoot this ?

Calculate -> Scripting ->

map_histogram(0) # or whatever your map number is

Do you see a sensible histogram?

If so, the problem is merely that you are looking at the wrong part of 
the cell or using the wrong contour level. Modern versions of coot go to 
centre of the cell if a model has not been loaded - this is usually the 
right place to find your molecule.


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