Hello Wei,

Maps you see in Coot are three-dimensional functions calculated on the grid. These functions are the finite resolution and finite quality images of electron (or nuclear, depending experiment) density in the crystal. They are calculated as a Fourier transform of Fourier map coefficients. In most cases these Fourier map coefficients are {2mFobs-DFmodel, PhiFmodel} and {mFobs-DFmodel, PhiFmodel}, that are complex numbers. Refinement programs like Refmac or phenix.refine output these map coefficients in MTZ formatted files, or you can calculated them given Fobs and atomic model using standalone programs, such as phenix.maps for instance.

Back to you original question: 'Create maximum entropy map' utility expected from you one of these MTZ files.

Hope this helps,
Pavel


On 9/20/14 10:41 AM, Wei Shi wrote:
The mtz file I loaded is from Phenix -> Reflection file editor with default settings using the cns.hkl file from xds. I am not sure how to get the MTZ with Fourier map coefficients. Thank you!

Best,
Wei

On Sat, Sep 20, 2014 at 12:39 PM, Pavel Afonine <[email protected]> wrote:
Most likely this is because you loaded MTZ with with no Fourier map coefficients.
Pavel


On 9/20/14 8:39 AM, Wei Shi wrote:
Thank you so much! Is 'Create maximum entropy map' in the latest nightly build that could create the omit map you guys suggested? I was trying to run it but got the error message 'No column labels specified'. In the columns labels it shows '---' and don't give me any option to change... I just loaded my mtz file and the ligand-free pdb file and left all other settings as default. Thank you so much!

Best,
Wei

On Wed, Sep 17, 2014 at 2:39 AM, Dale Tronrud <[email protected]> wrote:

   I don't believe I said he was the first.  He did develop an
implementation which has proven useful to a large number of people.

Dale

On 9/16/2014 8:52 PM, Nathaniel Echols wrote:
> On Tue, Sep 16, 2014 at 11:36 AM, Dale Tronrud <[email protected]
> <mailto:[email protected]>> wrote:
>
>     This sounds like Bricogne's maximum entropy maps.
>
>
> Maybe I'm misunderstanding this reference, but I don't think Bricogne
> was the first person to come up with the idea:
>
> https://www.researchgate.net/publication/232761305_Electron_density_images_from_imperfect_data_by_iterative_entropy_maximization
>
> which I think is just an extension of the application to X-ray astronomy
> described by Gull & Daniel (1978).
>
> -Nat
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