[phenixbb] Fo-Fc omit map for ligand in the protein-ligand structure

Pavel Afonine pafonine at lbl.gov
Sat Sep 20 10:57:35 PDT 2014


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 <pafonine at lbl.gov 
> <mailto:pafonine at lbl.gov>> 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
>>     <detBB at daletronrud.com <mailto:detBB at daletronrud.com>> 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
>>         <detBB at daletronrud.com <mailto:detBB at daletronrud.com>
>>         > <mailto:detBB at daletronrud.com
>>         <mailto:detBB at daletronrud.com>>> 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
>>         _______________________________________________
>>         phenixbb mailing list
>>         phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>>         http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>
>

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