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Hi,<br>
<br>
I agree: having different occupancies for covalently linked atoms
doesn't make much sense! If ligand is partially occupied then simply
refine its overall occupancy.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 2/7/16 14:44, Christian Roth wrote:<br>
</div>
<blockquote
cite="mid:CA+hUm_NW94zQO8SZn1yC0C1jB8nDz-vbiNNtdWjOjtOQ6Mo+SQ@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>Dear Chris,</div>
<div><br>
</div>
<div>personally I wouldn't go for different occupancies in one
ligand and set everything to 1 or everything to a values of
your choice (constraint groups necessary). I would also check
the electron density and the RSRZ for your ligands. The
B-factors look quite high. Concerning the outliers, that is
due to slight variations in the boundaries. Your outliers are
probably exactly on a boundary. I wouldn't worry too much
about that. They are fine.</div>
<div><br>
</div>
<div>Cheers</div>
<div><br>
</div>
<div>Christian</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sat, Feb 6, 2016 at 12:19 PM, Chris
Fage <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:cdfage@gmail.com" target="_blank">cdfage@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hello,
<div><br>
</div>
<div>The non-unity occupancies were scattered among
different glucose (and BICINE) molecules, as shown
below. But, again, I think the occupancy refinement
doesn't contribute much to the final model/maps.</div>
<div><br>
</div>
<div>Another concern of mind is that phenix.refine reports
no Ramachandran outliers in the results, but the plot
in�Coot lists 5. I'm tempted to trust Coot here and
attempt to fix these boundary cases.�<span></span></div>
<div><br>
</div>
<div>Best,</div>
<div>Chris</div>
<div><br>
</div>
<div>
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</div>
</div>
<div class="HOEnZb">
<div class="h5">
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Feb 5, 2016 at 7:34
PM, Christian Roth <span dir="ltr"><<a
moz-do-not-send="true"><a class="moz-txt-link-abbreviated" href="mailto:christianroth034@gmail.com">christianroth034@gmail.com</a></a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<p dir="ltr">Hi Chris, what would concern me is
that one glucose have atoms with different
occupancies or all of them. That is chemically
unlikely. You should define sensible constraint
groups, I think.</p>
<p dir="ltr">Cheers Christian</p>
<div class="gmail_quote">
<div>
<div>On 5 Feb 2016 18:09, "Chris Fage" <<a
moz-do-not-send="true"><a class="moz-txt-link-abbreviated" href="mailto:cdfage@gmail.com">cdfage@gmail.com</a></a>>
wrote:<br type="attribution">
</div>
</div>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div>
<div>
<div dir="ltr">Hi Pavel,
<div><br>
</div>
<div>The B-factors of these atoms are
quite high (most are 100+), so maybe
the occupancy is compensating as you
said. After refinement, the maps don't
look much different. Perhaps it's not
worth bothering with occupancy
refinement, then?</div>
<div><br>
</div>
<div>I think you got my question. I was
asking if it is unusual that only 5/93
occupancies were refined to values
other than 0 or 1.</div>
<div><br>
</div>
<div>Best,</div>
<div>Chris</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Feb 5,
2016 at 6:38 PM, Pavel Afonine <span
dir="ltr"><<a
moz-do-not-send="true"><a class="moz-txt-link-abbreviated" href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a></a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">Hi Chris,<span><br>
<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
I've built several glucose
molecules from my cryosolution
into regions of weaker electron
density. Attempting to refine
the occupancies of the
corresponding atoms, I set the
value of each to 0.25 in the pdb
file. However, after running
phenix.refine, most of the atoms
still have occupancies of 1.00:<br>
</blockquote>
<br>
</span>
perhaps they are fully occupied but
highly mobile which explains weak
density? Or B-factor refines to
larger value so that occupancy tries
to compensate? How maps look like
after refinement?<span><br>
<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
14 atoms with occ = 0.00<br>
5 atoms with 0.00 < occ <
1.00<br>
74 atoms with occ = 1.00<br>
<br>
Is this unusual?<br>
</blockquote>
<br>
</span>
Do you mean is it unusual to have 5
atoms in your structure with
occupancies between 0 and 1? Hm.. I
don't know, may be not! I think I'm
not understanding what's the real
question here..<span><font
color="#888888"><br>
<br>
Pavel<br>
<br>
</font></span></blockquote>
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