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Hi Mary,<br>
<br>
there was almost exactly the same question on phenixbb a couple of
days ago.<br>
<br>
Try doing it differently and see what happens:<br>
<br>
step 1: <br>
remove ligand from PDB file <br>
<br>
phenix.pdbtools model.pdb remove="chain X and resseq 123"<br>
<br>
or set its occupancy to 0 (which is not 100% equivalent but close):<br>
<br>
phenix.pdbtools model.pdb occupancy.set=0 selection="chain X and
resseq 123"<br>
<br>
step 2:<br>
run SA refinement using phenix.refine:<br>
<br>
phenix.refine model.pdb data.mtz model_no_ligand.pdb
simulated_annealing=true<br>
<br>
step 3: load a map created by above run into Coot: how different it
is from the map that you get from phenix.autobuild run?<br>
<br>
Pavel.<br>
<br>
PS1.:<br>
I will add a test that will assert that both ways (the above one and
using phenix.autobuild) give similar results.<br>
<br>
PS2.:<br>
You probably meant mFo-DFc map or 2mFo-DFc (and not 2Fo)?<br>
<br>
<br>
On 6/3/11 7:21 AM, Desi Mail wrote:
<blockquote
cite="mid:BANLkTikTo5O=uzXUDrU8AupGtqGOGBb8iQ@mail.gmail.com"
type="cite">Hi everybody,<br>
<br>
I would like to calculate the omit map around the ligand. I
followed the documentation<br>
<a moz-do-not-send="true"
href="http://www.phenix-online.org/documentation/autobuild.htm#anch159">http://www.phenix-online.org/documentation/autobuild.htm#anch159</a><br>
<br>
But the 2Fo density around the ligand is very poor.<br>
<br>
Any help is appreciated.<br>
<br>
Thanks<br>
Mary <br>
<h5>Make a SA-omit map around atoms in target.pdb</h5>
<p><a moz-do-not-send="true" name="anch168"
id="Make_a_SA-omit_map_around_atoms_in_target_pdb_2"></a>
</p>
<pre style="">phenix.autobuild data=data.mtz model=coords.pdb omit_box_pdb=target.pdb composite_omit_type=sa_omit
</pre>
Coefficients for the output omit map will be in the file
resolve_composite_map.mtz in the subdirectory OMIT/ .
An additional map coefficients file omit_region.mtz will show you
the
region that has been omitted. (Note: be sure to use the weights in
both
resolve_composite_map.mtz and omit_region.mtz).
<br>
<pre wrap="">
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</pre>
</blockquote>
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