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Hi Jason,<br>
<br>
Oleg is correct, you can assign the ligand and PHE different
non-blanc altlocs (say A and B). In this case PHE and ligand will
not 'see' each other via repulsion term of restraints. Also, their
occupancies will be refined independently and will be constrained to
be within 0 and 1, but it will not make sure that they add up to 1.
If you want them to add up to 1, then make a parameter file with a
constrained group as described in one of examples here:<br>
<br>
"13 typical occupancy refinement scenarios and available options in
phenix.refine"<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/newsletter/">http://phenix-online.org/newsletter/</a><br>
<br>
You can do it in the GUI too.<br>
<br>
Let us know if you more questions or problems!<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 3/2/18 02:57, Oleg Sobolev wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CADd3otGuVs-pmOoSsTeO6kSZM91g5ZVn8YnQkFUCNdW2KNA72w@mail.gmail.com">
<div dir="ltr">Hi Jason,
<div><br>
</div>
<div class="gmail_extra">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div style="margin:0px;line-height:normal">
<div
style="margin:0px;font-size:8px;line-height:normal"><br>
</div>
</div>
<div>The ligand and APHE got pushed away from one
another and off of their respective densities.
Occupancies for both were reduced to 0.5 for the
refinement. What am I doing wrong here? Does the
ligand need to have an altloc as well? But I don’t see
an alternative conformation. </div>
</div>
</blockquote>
<div><br>
</div>
<div>Yes, the ligand also needs an altloc, and it should be
different from PHE altloc. This way the refinement will
know that these atoms don't see each other. You don't have
to put two alternative conformations for the ligand, you
can have just one with partial occupancy (<1.0) which
will mean that the ligand is not always there.</div>
<div> </div>
<div>Best regards,</div>
<div>Oleg Sobolev.</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div style="word-wrap:break-word">
<br>
<div>
<blockquote type="cite">
<div>On Feb 28, 2018, at 5:35 PM, van den Bedem,
Henry <<a
href="mailto:vdbedem@slac.stanford.edu"
target="_blank" moz-do-not-send="true">vdbedem@slac.stanford.edu</a>>
wrote:</div>
<br
class="m_8858005827093028639Apple-interchange-newline">
<div>
<div class="m_8858005827093028639WordSection1"
style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
If the phe is a gatekeeper, shouldn’t the
ligand be refined at partial occupancy; i.e.
occupancies not necessarily have to ‘add up’
as you suggest? Maybe this link is helpful
too:<span
class="m_8858005827093028639Apple-converted-space"> </span><a
href="http://www.biorxiv.org/content/early/2018/01/24/253419"
style="color:rgb(149,79,114);text-decoration:underline"
target="_blank" moz-do-not-send="true">www.biorxiv.org/content/<wbr>early/2018/01/24/253419</a></div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
</div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
H</div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
</div>
<div style="border-style:solid none
none;border-top-width:1pt;border-top-color:rgb(181,196,223);padding:3pt
0in 0in">
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<b><span style="font-size:12pt">From:<span
class="m_8858005827093028639Apple-converted-space"> </span></span></b><span
style="font-size:12pt"><<a
href="mailto:phenixbb-bounces@phenix-online.org"
style="color:rgb(149,79,114);text-decoration:underline" target="_blank"
moz-do-not-send="true">phenixbb-bounces@<wbr>phenix-online.org</a>>
on behalf of "Phan, Jason" <<a
href="mailto:jason.phan@vanderbilt.edu"
style="color:rgb(149,79,114);text-decoration:underline" target="_blank"
moz-do-not-send="true">jason.phan@vanderbilt.edu</a>><br>
<b>Date:<span
class="m_8858005827093028639Apple-converted-space"> </span></b>Wednesday,
February 28, 2018 at 1:30 PM<br>
<b>To:<span
class="m_8858005827093028639Apple-converted-space"> </span></b>"<a
href="mailto:phenixbb@phenix-online.org"
style="color:rgb(149,79,114);text-decoration:underline" target="_blank"
moz-do-not-send="true">phenixbb@phenix-online.<wbr>org</a>"
<<a
href="mailto:phenixbb@phenix-online.org"
style="color:rgb(149,79,114);text-decoration:underline" target="_blank"
moz-do-not-send="true">phenixbb@phenix-online.org</a>><br>
<b>Subject:<span
class="m_8858005827093028639Apple-converted-space"> </span></b>[phenixbb]
Overlapping ligand-protein side chain
density</span></div>
</div>
<span class="">
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
</div>
</div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<a
name="m_8858005827093028639__MailOriginalBody"
moz-do-not-send="true">All, <span
class="m_8858005827093028639Apple-converted-space"> </span></a></div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span> </span></div>
</div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span>A piece of a ligand and the side
chain of a “gate-keeper” Phe occupy the
same space with well-defined features
observed for both (resolution is 1.7 A).
It looks about 50:50. How do you refine
both ligand and protein side chain in
this case? A couple of phenixbb
suggestions for dealing with
ligand-ligand overlapping density have
been considered. With the first
suggestion, the two entities still
clashed and moved apart off of their
respective densities. The second
suggestion is not applicable in this
case since the other molecule is not a
ligand but part of the protein but it
was tested anyway. Although there was no
bumping, the occupancies don’t add up,
resulting in a big blob of negative
density around the ligand piece. </span></div>
</div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span> </span></div>
</div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span>------------------------------</span></div>
</div>
<div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span>Only two comments:</span></div>
</div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span> </span></div>
</div>
<ol start="1"
style="margin-bottom:0in;margin-top:0in"
type="a">
<li class="MsoNormal" style="margin:0in
0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span>At that resolution, constrained
group occupancy refinement should work
reasonably well (provided you can
model the 2 entities). Then you also
do not have clashes between the
molecules, because Occ(A)+Occ(B)=1,
meaning when one (A) is there, the
other one (B) is not. This works with
refmac (external keyword file); if you
need more sophisticated occupancy
re/constraints SHELXL may offer more
opportunities.</span></li>
<li class="MsoNormal" style="margin:0in
0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span>There is no necessity for the two
NCS copies of the binding site to look
exactly the same (non-equivalent).
Maybe there is a good reason/story
(accessibility, contacts etc) for one
site to be occupied differently than
the other one. </span></li>
</ol>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span> </span></div>
</div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span>Best, BR</span></div>
</div>
</div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span>——————————————</span></div>
</div>
<div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span><span
style="font-size:10.5pt;font-family:Helvetica">Modeling
two molecules that occupy
overlapping binding sites in a
structure simply involves
designating them as alternate
conformers, with the same chain and
residue number, and an occupancy
that sums to 1.0. For example, if
you have an AMP and an ADP that
occupy the same binding site, you
would define them as</span></span></div>
</div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span><span
style="font-size:10.5pt;font-family:Helvetica"> </span></span></div>
</div>
<div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span><span
style="font-size:10.5pt;font-family:Courier">AAMP
B 501</span></span><span><span
style="font-size:10.5pt;font-family:Helvetica"></span></span></div>
</div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span><span
style="font-size:10.5pt;font-family:Courier">BADP
B 501</span></span><span><span
style="font-size:10.5pt;font-family:Helvetica"></span></span></div>
</div>
</div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span><span
style="font-size:10.5pt;font-family:Helvetica"> </span></span></div>
</div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span><span
style="font-size:10.5pt;font-family:Helvetica">and
initially set the occupancies for
the atoms in each conformer to the
ratio (50:50, 30:70, etc.) that you
observe in the density.</span></span></div>
</div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span><span
style="font-size:10.5pt;font-family:Helvetica"> </span></span></div>
</div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span><span
style="font-size:10.5pt;font-family:Helvetica">Refinement
in this manner is straightforward in
PHENIX.</span></span></div>
</div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span><span
style="font-size:10.5pt;font-family:Helvetica"> </span></span></div>
</div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span><span
style="font-size:10.5pt;font-family:Helvetica">Diana</span></span></div>
</div>
<div>
<div style="margin:0in 0in
0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span><span
style="font-size:10.5pt;font-family:Helvetica">----------------------------</span></span></div>
</div>
</div>
</span></div>
</div>
</blockquote>
</div>
<br>
</div>
<br>
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