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Hi Alex,<br>
<br>
why use a cannon to kill a fly? phenix.refine is for refinement not
map calculation. I suggest to use more specific tools. phenix.maps
should do it, for example.<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/documentation/reference/phenix_maps.html">http://phenix-online.org/documentation/reference/phenix_maps.html</a><br>
<br>
Pavel<br>
<br>
<blockquote
cite="mid:CAA5EDMTZNw2yyhWmv0Ae3wnY2VfjBVa0vLf=0ty=L1Rjt-7ngA@mail.gmail.com"
type="cite">
<div dir="ltr">
<div class="gmail_quote">
<div dir="ltr">I am trying to get the difference electron
density maps for residues with multiple conformations after
I set the occupancy of their atoms to 0.
<div>My main goal is to visualize the green positive density
peaks that should appear for the atoms whose occupancy I
set to 0.</div>
<div>However, when I run the phenix.refine command (doing
all of this via cli, not gui), the output pdb file </div>
<div><br>
</div>
<div><br>
</div>
<div>I will try to illustrate my process and problem with an
example that works fine and one that doesn't, side by
side, step by step.</div>
<div>
<ol>
<li>I generate a pdb file that has a chosen residue set
to occupancy 0. See
'pdb_1agy_res_SER_resID_120_del.pdb' and
'pdb_1agy_res_SER_resID_129_del.pdb'. As you can see,
the former has SER 120 set to 0 occupancy and has one
conformation, and the latter has SER 129 set to 0
occupancy for BOTH of its conformations. Both files
are correct up to this point.</li>
<li>I then execute the following command:</li>
</ol>
phenix.refine <b>pdb_del_file</b> <b>mtz_file</b> main.number_of_macro_cycles=5
output.write_eff_file=False output.write_geo_file=False
output.write_def_file=False
refinement.input.xray_data.r_free_flags.generate=True
--overwrite
<ul>
<li>with <b style="font-weight:bold">mtz_file </b>set
to '1agy.mtz' (from the PDB) and <b>pdb_del_file</b> set
to either 'pdb_1agy_res_SER_resID_120_del.pdb' and
'pdb_1agy_res_SER_resID_129_del.pdb'.</li>
</ul>
</div>
<div>
<ul>
<li>This results in 2
files pdb_1agy_res_SER_resID_XXX_del_refine_001.mtz
and pdb_1agy_res_SER_resID_XXX_del_refine_001.pdb.
Comparing these pdb files, you can see that the
occupancy for SER 120 remains set to 0 (which is what
I want), but the occupancies for the 2 conformers for
SER 129 have been filled in by phenix (not what I
want) somewhere during the refinement process. As a
result, I get the desired difference peaks for SER
120, but not for SER 129 (which seems to be averaged
out).</li>
</ul>
Other than deleting the 2nd conformation for SER 129, is
there a way to solve this problem, preferably via command
line arguments/flags?</div>
<div><br>
</div>
<div>Thanks,<br>
Alex</div>
</div>
</div>
</div>
<br>
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<br>
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