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<p style="margin-top:0;margin-bottom:0">Hi Pavel/ CCTBXBB,</p>
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<p style="margin-top:0;margin-bottom:0">I have used phenix.fmodel to generate structure factors (Fcalc)
<span>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:</span></p>
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<p style="margin-top:0;margin-bottom:0"><span>phenix.fmodel data_column_label="F,SIGF" merged.pdb free.mtz type=real</span><br>
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<p style="margin-top:0;margin-bottom:0"><span>In the merged.pdb file I set the isotropic B-factor (through u_iso)
<span>to a known value (i.e. b=40)</span>, 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.
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<p style="margin-top:0;margin-bottom:0"><span><span>Does phenix.fmodel generate its mtz regarding the B factor of individual atoms?
</span><br>
</span></p>
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</span></p>
<p style="margin-top:0;margin-bottom:0"><span>To give context to this question:<br>
</span></p>
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</span></p>
<p style="margin-top:0;margin-bottom:0">I then use these Fcalc values to test a brute force search of occupancy and b_factor values. <span>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)|.
</span></p>
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<p style="margin-top:0;margin-bottom:0">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. </p>
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<p style="margin-top:0;margin-bottom:0">Thanks</p>
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<p style="margin-top:0;margin-bottom:0">Elliot<br>
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<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Pavel Afonine <pafonine@lbl.gov><br>
<b>Sent:</b> 06 April 2018 01:07<br>
<b>To:</b> cctbx mailing list; Elliot Nelson<br>
<b>Cc:</b> Pearce, N.M. (Nick); Frank Von Delft<br>
<b>Subject:</b> Re: [cctbxbb] mmtbx/examples/simulate_experimental_data.py</font>
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<div style="background-color:#FFFFFF">Hi Elliot,<br>
<br>
<blockquote type="cite">
<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">I'm trying to generate some simulated mtz files. My main aim is to test a script which looks to determine ligand occupancy (<a href="https://github.com/nelse003/exhaustive_search/blob/master/exhaustive_search.py" target="_blank" id="LPlnk257469" class="OWAAutoLink" previewremoved="true">https://github.com/nelse003/exhaustive_search/blob/master/exhaustive_search.py</a>)
by looking at |Fo-Fc| over the ligand/ ground-state the ligand replaces. <br>
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</blockquote>
<br>
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?<br>
<br>
<blockquote type="cite">
<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">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.
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</blockquote>
<br>
OK. <br>
<br>
phenix.fmodel model.pdb high_res=2.3 <br>
<br>
will calculate Fcalc from given atomic model in model.pdb file. You can pretend it to be Fobs:<br>
<br>
phenix.fmodel model.pdb high_res=2.3 type=real<br>
<br>
There is a more sophisticated tool that will actually go to some length trying to mimic actual Fobs data<br>
<br>
phenix.fake_f_obs<br>
<br>
It's not documented anywhere.. So have a look at the code to see what it actually does.<br>
<br>
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.<br>
<br>
All the best,<br>
Pavel<br>
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