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Hi Wei,<br>
<br>
I think I replied to a very similar question on this mailing list
some time ago (in August).<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>
At some point I've spent a day doing tests to exemplify all this.<br>
<br>
Here is how to do this right. You need to define a box around the
ligand that covers the ligand itself and some volume around it, then
omit all scattering from inside the box (ligand and bulk-solvent!),
and then use this model with box omitted to calculate residual
synthesis. <br>
<br>
I don't think we have a ready to use tool in Phenix to do this. It's
possible to do this with some scripting using CCTBX.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 9/13/14 2:40 PM, Wei Shi wrote:<br>
</div>
<blockquote
cite="mid:CA+Sz7q4RKmm7q2vn+3-Bn94Bev7z=c12CmJq6B3KR4zTJdgoMA@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>
<div>
<span style="font-family:tahoma,sans-serif"><font><span
style="background-color:rgb(255,255,255)"><span
style="color:rgb(33,33,33);background-image:none;background-repeat:repeat">Hi
all, <br>
I am working with a protein dimer-ligand structure
(resolution: 2.8</span></span><span
style="background-color:rgb(255,255,255)"><span
style="color:rgb(33,33,33);background-image:none;background-repeat:repeat">Å)
and am going to make a figure showing the </span></span><span
style="background-color:rgb(255,255,255)"><span
style="color:rgb(33,33,33);background-image:none;background-repeat:repeat">bound
ligand superimposed with the electron density
(Fo-Fc) map obtained after
omit refinement</span></span>. <br>
</font></span></div>
<span style="font-family:tahoma,sans-serif"><font>What I did
is to make the ligand-free structure model and then use
Phenix.refine using the following parameters plus
simulated annealing (torsion angle) or (Cartesian): <br>
</font></span></div>
<font color="black"><span style="background-color:white"
dir="ltr"><span
style="font-weight:normal;font-variant:normal;text-transform:none">
<div style="margin-top:0px;margin-bottom:0px">Default: XYZ
coordinates + Real-space+ Individual B factors +
Occupancies.</div>
<div style="margin-top:0px;margin-bottom:0px">Also click:
Optimize X-ray/stereochemistry weight + Optimize
X-ray/ADP weight + Secondary structure restraints + NCS.
<br>
<br>
</div>
<div style="margin-top:0px;margin-bottom:0px">Contoured at
2<span class="">σ</span>, the Fo-Fc map generated show
green density for most part of the ligand, but for
several atoms in the middle of the ligand, the green
density is missing... <font color="black"><span
style="background-color:white" dir="ltr"><span
style="font-weight:normal;font-variant:normal;text-transform:none">It's
like this: some atoms have green density and the
next few no green density and then a couple few
has green density and then a couple more no green
denisty....</span></span></font> The missing green
density usually means that part is disordered in the
structure, right? I am not sure why the density is
missing for some atoms in the middle of the ligand. It
would makes more sense if the missing green density is
at the end of the ligand...<br>
<br>
</div>
<div style="margin-top:0px;margin-bottom:0px">Does anyone
happen to have any clue about what it means for the
green density missing in my case? <br>
<br>
</div>
<div style="margin-top:0px;margin-bottom:0px">Also, I am
not sure whether I did the omit refinement right:<br>
</div>
<div style="margin-top:0px;margin-bottom:0px">(1). For
simulated annealing, it has two options, one is
Cartesian and the other is Torsion angle, and it's said
that torsion angle is more suitable of low resolution
data. Is there any difference about which one to choose
in my case?<br>
(2). Is it Okay to run the omit refinement in the
presence of the following parameters as I did: <br>
<font color="black"><span style="background-color:white"
dir="ltr"><span
style="font-weight:normal;font-variant:normal;text-transform:none">Optimize
X-ray/stereochemistry weight + Optimize X-ray/ADP
weight + Secondary structure restraints + NCS.<br>
<br>
</span></span></font></div>
<div style="margin-top:0px;margin-bottom:0px"><font
color="black"><span style="background-color:white"
dir="ltr"><span
style="font-weight:normal;font-variant:normal;text-transform:none">Thank
you so much!<br>
<br>
Best, <br>
Wei <br>
</span></span></font></div>
<div style="margin-top:0px;margin-bottom:0px"><font
color="black"><span style="background-color:white"
dir="ltr"><span
style="font-weight:normal;font-variant:normal;text-transform:none"><br>
</span></span></font></div>
</span></span></font></div>
<br>
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