[cctbxbb] mmtbx/examples/simulate_experimental_data.py

Oleg Sobolev osobolev at lbl.gov
Thu Apr 5 12:10:52 PDT 2018


Hi Elliot,

It looks like you want to calculate Fo-Fc map and have it in .mtz format. I
would suggest to have a look at phenix.maps tool (living in
cctbx_project/mmtbx/command_line/maps.py).

I believe confusion happened because .mtz format can store various things:
experimental data (Fobs), map coefficients or both. You were generating
fake experimental data, which cannot be displayed in Coot because it is not
a map.

Hope it helps,

Best regards,
Oleg Sobolev.

On Thu, Apr 5, 2018 at 1:24 AM, Elliot Nelson <elliot.nelson at dtc.ox.ac.uk>
wrote:

> Hi All,
>
> I'm trying to generate some simulated mtz files.  My main aim is to test a
> script which looks to determine ligand occupancy (
> https://github.com/nelse003/exhaustive_search/blob/master/
> exhaustive_search.py) by looking at |Fo-Fc| over the ligand/ ground-state
> the ligand replaces.
>
> To test this I would like to generate mtz files from pdb models with a
> ligand occupancy that has varied between 0-1, which the above script would
> hopefully recover the occupancy.
>
> I have tried to use mmtbx/examples/simulate_experimental_data.py (
> https://github.com/cctbx/cctbx-playground/blob/
> 8f23c190a9f8d2ed2b5845385f568f3233c16132/mmtbx/examples/
> simulate_experimental_data.py ) to generate an mtz file.
>
> So far I have been able to generate mtz files using the
> simulate_experimental_data.py, these have the columns:
>
>  H K L FOBS(+) SIGFOBS(+) FOBS(-) SIGFOBS(-)
>
> I can use this outputted mtz for running tests of my scripts ,However as
> this has no PHI columns, I cannot display this in coot. I have tried to add
> the phi column from the refined mtz of the orignal data using CAD, but have
> not yet managed to do this succesfully.
>
> I feel that this may be an overcomplicated, and potentially superseded way
> of generating simulated mtz data.  Any advice on alternatives would be
> really useful?
>
> Apologies if this is not very clear.
>
> Thanks
>
> Elliot Nelson
>
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> cctbxbb at phenix-online.org
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>
>
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