[cctbxbb] mmtbx/examples/simulate_experimental_data.py

[Elliot Nelson]

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I feel that this may be an overcomplicated, and potentially superseded way of generating simulated mtz data.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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