[cctbxbb] mmtbx/examples/simulate_experimental_data.py

[Elliot Nelson]

Hi Pavel/ CCTBXBB,


I have used phenix.fmodel to generate structure factors (Fcalc) from given atomic model in merged.pdb file. As previously suggested I am using the type=real flag to populate the Fobs with these Fcalc values:


phenix.fmodel data_column_label="F,SIGF" merged.pdb free.mtz type=real


In the merged.pdb file I set the isotropic B-factor (through u_iso) to a known value (i.e. b=40), and occupancy of the involved ligand/ground state. i.e Occupancy of ligand/ bound state atoms (0.05) and ground state atoms (0.95), all with B Factor =40.


Does phenix.fmodel generate its mtz regarding the B factor of individual atoms?


To give context to this question:


I then use these Fcalc values to test a brute force search of occupancy and b_factor values.  I am searching through Fcalc(1)-Fcalc(2) maps, where Fcalc(1) is the Fcalc generated by phenix.fmodel. Fcalc(2) is generated from the same pdb file, but with occupancy and u_iso of atoms in the ligand/ground state varied (occ 0.05 to 0.95, u_iso 0.2 to 1.2). After this search, I look at the mean over points near bound/ground state of |Fcalc(1)-Fcalc(2)|.


My test should be able to uniquely identify the occupancy and B factor values supplied in the merged.pdb file. I can recapitulate the expected occupancy, however I cannot recapitulate this supplied B factor.


Thanks


Elliot


________________________________
From: Pavel Afonine <pafonine at lbl.gov>
Sent: 06 April 2018 01:07
To: cctbx mailing list; Elliot Nelson
Cc: Pearce, N.M. (Nick); Frank Von Delft
Subject: Re: [cctbxbb] mmtbx/examples/simulate_experimental_data.py

Hi Elliot,

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.

it isn't clear what you are trying to do.. What you call "simulated mtz files". MTZ is just a file format.. What you expect in these MTZ files?

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.

OK.

phenix.fmodel model.pdb high_res=2.3

will calculate Fcalc from given atomic model in model.pdb file. You can pretend it to be Fobs:

phenix.fmodel model.pdb high_res=2.3 type=real

There is a more sophisticated tool that will actually go to some length trying to mimic actual Fobs data

phenix.fake_f_obs

It's not documented anywhere.. So have a look at the code to see what it actually does.

If you describe what exactly you want to do and how you want to do it, then we may be able to come up with a more tailored to your goal solution.

All the best,
Pavel

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