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Hi Elliot,<br>
<br>
<blockquote type="cite"
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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 style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"><span>phenix.fmodel
data_column_label="F,SIGF" merged.pdb free.mtz type=real</span><br>
</p>
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</blockquote>
<br>
flag 'type=real' converts complex value Fcalc to real values.<br>
<br>
<blockquote type="cite"
cite="mid:LO1P123MB0004B1897DD6C80E1C7D862180980@LO1P123MB0004.GBRP123.PROD.OUTLOOK.COM">
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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.�
</span></p>
<p style="margin-top:0;margin-bottom:0"><span><br>
</span></p>
<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>
</div>
</blockquote>
<br>
To calculate Fcalc you need:<br>
- coordinates;<br>
- ADP (B-factors);<br>
- occupancies;<br>
- atom scattering type (element and charge if available).<br>
<br>
(Figure 1 on page 37 here:
<a class="moz-txt-link-freetext" href="http://phenix-online.org/newsletter/CCN_2015_07.pdf">http://phenix-online.org/newsletter/CCN_2015_07.pdf</a>)<br>
<br>
that is all information from ATOM record of your PDB file is used
(except unnecessary decorators, such as chain and atom labels).<br>
<br>
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<p style="margin-top:0;margin-bottom:0"><span>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span></span><span>To
give context to this question:</span><br>
<span>
</span>
</p>
<p style="margin-top:0;margin-bottom:0"><span><br>
</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>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<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. <br>
</p>
</div>
</blockquote>
<br>
Since you have all controlled numerical setup, as usual in such
cases try to simplify the task by varying one parameter at a time.
For example, make sure occupancy search works (given fixed B), then
make sure B search works (given fixed q), then vary both and there
is no reason that should then not work.<br>
<br>
Of course there are plenty of details involved here that make this
easy or tricky, such as what optimization target you use: real or
reciprocal space? If real space, do you make sure to scale maps by
volume (absolute scale) and not by rms? What's size of region where
you compute 'mean over grid points'? etc etc etc etc. <br>
<br>
Can't comment more without having more technical details..<br>
<br>
Good luck,<br>
Pavel<br>
�<br>
<br>
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