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<div class="moz-text-flowed" style="font-family: -moz-fixed;
font-size: 12px;" lang="x-western">Hello Bishal,
<br>
<br>
as discussed before, computing ligand-omit map is tricky.
<br>
<br>
Quoting my previous email:
<br>
<br>
"""
<br>
There are two commonly used options for omitting the ligand in
order to demonstrate its presence/absence in Fo-Fc OMIT map:
<br>
<br>
1) Physically remove the ligand from PDB file. Then do some
refinement and calculate Fo-Fc map.
<br>
<br>
2) Keep ligand in the file, set its occupancy to zero. Then,
again, do some refinement and calculate Fo-Fc map. In this case
you may want to ask refinement program to not move the ligand or
move it only a little.
<br>
<br>
Now, here is why these two options are poor and will not give you
what you want.
<br>
<br>
In the first case the bulk-solvent mask will be set in the ligand
region and therefore it will mask ligand density (bulk-solvent
will be filled into the ligand region). Depending on the strength
of ligand density it may be masked completely or deteriorated.
<br>
<br>
If you follow the second option you will always get positive
density in ligand area. This density may correspond to
bulk-solvent, ligand or mixture of both. That is there will be no
simple way to differentiate whether this density arises from the
ligand or bulk-solvent.
<br>
"""
<br>
<br>
Dale Tronrud offered a great alternative option:
<br>
<br>
"""
<br>
An alternative you might want to consider is what I call the
<br>
"discovery map". At some point in the refinement process there
was a
<br>
map that convinced YOU that this ligand was present. You should
be
<br>
the hardest person to be convinced so that map will be both an
omit
<br>
map (because the model had been refined without the ligand prior
to
<br>
this) and clear enough to satisfy the reader.
<br>
"""
<br>
<br>
Now, recently I improved composite OMIT map calculation in
<br>
<br>
phenix.composite_omit_map
<br>
<br>
tool, see picture that illustrates how it works:<br>
<br>
<a class="moz-txt-link-freetext" href="https://www.dropbox.com/s/dbp8e0348v5p78h/fig_6.png?dl=0">https://www.dropbox.com/s/dbp8e0348v5p78h/fig_6.png?dl=0</a><br>
<br>
I think at present that's the best option to follow if for some
reason you cannot follow Dale's suggestion.
<br>
<br>
Pavel
<br>
<br>
<br>
On 11/13/14 6:58 AM, Singh, Bishal wrote:
<br>
<blockquote type="cite" style="color: #000000;">Hello everybody,
<br>
I am generating figures showing the electron density map
around the ligands. I deleted the ligands from final co-ordinate
file and then performed refinement with identical parameters as
before while keeping simulated annealing=true. I shall be
thankful if someone could suggest me whether I consider mFo-DFc
map or 2mFo-DFc map or both. Kindly also tell me the minimum
acceptable contour level required for showing difference map.
All structures are at 1.4 - 2.0 angstrom resolutions.
<br>
<br>
Regards,
<br>
Bishal </blockquote>
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