Hi Wojtek, attached is a simple Python script that will read in your EM map (in ccp4 format; I can trivially change the script so it reads x-plor map too) and it will write out MTZ file containing:
- complex array of Fobs (Fobs_cmpl), which is just a Fourier transform of
the input map;
- real array of Fobs, which is Fobs = abs(Fobs_cmpl);
- phases of Fobs_cmpl as HL coefficients.
You can use these Fobs and HL in phenix.refine refinement. In this case
phased ML target function (MLHL) will be used for refinement.
To run the script:
- edit it to specify input map file name and high resolution (d_min);
- run it as
phenix.python run.py
- have a look at output file content:
phenix.mtz.dump map_data.mtz
Pavel
P.S.: The MTZ file you sent me off-list was wrong.
On Fri, Jul 13, 2012 at 8:28 AM, Wojtek Potrzebowski <wpotr...@genesilico.pl
> wrote:
> Dear all,
> I want to refine a model of the complex that consists of rigid subunits
> using an electron microscopy electron density map.
> I've tried to use phenix for this purpose. Thus I have to back-FT the
> electron density map to a mtz reflection file.
> I've experienced problem using sfall for this purpose, but cinvfft has
> done a job (I can read a resulting file with mtzdmp).
> However phenix doesn't read this file properly (data labels box is empty).
> Can anyone help me on this, please?
> I am looking forward to hearing from you,
> Wojtek
>
run.py
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