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P.S.: In case you want the occupancies to add up to 1, the
constrained group will be looking like this:<br>
<br>
refinement {<br>
refine {<br>
occupancies {<br>
constrained_group {<br>
selection = chain A and resseq 123 and resname LIG<br>
selection = chain B and resseq 890 and altloc A<br>
}<br>
}<br>
}<br>
}<br>
<br>
Note two selections in the group, meaning that occupancy of (chain A
and resseq 123 and resname LIG) will be refined and constraied
between 0 and 1, occupancy of (chain B and resseq 890 and altloc A)
will be refined and constraied between 0 and 1, and occupancy of
(chain A and resseq 123 and resname LIG) plus occupancy of (chain B
and resseq 890 and altloc A) will be 1.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 3/2/18 06:59, Pavel Afonine wrote:<br>
</div>
<blockquote type="cite"
cite="mid:653c5c12-904a-34fe-2f3a-ba641efc2835@lbl.gov">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
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/"
moz-do-not-send="true">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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