<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi All,<br>
<br>
FWIW, this scenario is described in <br>
<br>
"13 typical occupancy refinement scenarios and available options in
phenix.refine" article here<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/newsletter/">http://phenix-online.org/newsletter/</a><br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 1/15/16 12:30, Helena Taberman
wrote:<br>
</div>
<blockquote cite="mid:128D914F-94DF-494F-829A-4BF561BF3604@uef.fi"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<div><br>
</div>
<div>Thank you for your help indeed! Renaming them would have
never crossed my mind!</div>
<div><br>
</div>
<div>Best regards,</div>
<div><br>
</div>
<div>Helena</div>
<div><br>
On 15.1.2016, at 22.27, Oleg Sobolev <<a
moz-do-not-send="true" href="mailto:osobolev@lbl.gov"><a class="moz-txt-link-abbreviated" href="mailto:osobolev@lbl.gov">osobolev@lbl.gov</a></a>>
wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>
<div dir="ltr">Hi Helena,
<div><br>
</div>
<div>I just spotted that residue 249 is close to 252. To
resolve this, you will have to rename conformations of
residue 249 (exchange A and B altlocs), assing all partial
occupancies to 0.5 to make things simple and add it to
selections:</div>
<div><br>
</div>
<div>
<div>selection = chain A and (resseq 252 or resseq 249)
and altloc A</div>
<div>selection = chain A and (resseq 252 or resseq 249)
and altloc B or chain S and resseq 1702 and altloc B</div>
</div>
<div><br>
</div>
<div>Renaming is necessary because conformaion B of residue
249 is close to conformation B of residue 252.</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Oleg Sobolev.</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Jan 15, 2016 at 12:13 PM,
Oleg Sobolev <span dir="ltr">
<<a moz-do-not-send="true"
href="mailto:osobolev@lbl.gov" target="_blank">osobolev@lbl.gov</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">Hi Helena,
<div><br>
</div>
<div>The problem was in altlocs, occupancies and
selections.<br>
</div>
<div><br>
</div>
<div>First, simple case of 249 residue. I don't see
why residue 249 is relevant to 252 or to water 1702
because it is rather far from them. Therefore it
should be treated separately. Residue 249 simply has
2 alternative conformations of side chain (including
CA atom). We set occupancy of A and B conformations
to 0.5 (that is in your file). Also we need to set
occupancy to 1 for N, C and O atoms in this residue
to prevent their occupancy from refinement (in your
file they are also present with 0.5 occupancy).</div>
<div><br>
</div>
<div>The second case: coupled conformations of 252 and
water 1702.</div>
<div>For partially occupied water molecules you also
need to define appropriate altloc. In your case it
is present only when the residue 252 in B
conformation, therefore water molecule also should
have B altloc and partial occupancy (the same as B
conformation of residue 252, 0.49). The residue 252
is split to alternative conformations completely,
and this is OK. Next, to let phenix.refine know that
these conformations are coupled, you need the
following parameter file:</div>
<div>
<div>refinement {</div>
<div>� refine {</div>
<div>� � occupancies {</div>
<div>� � � constrained_group {</div>
<div>� � � � selection = chain A and resseq 252 and
altloc A</div>
<div>� � � � selection = chain A and resseq 252 and
altloc B or \</div>
<div>� � � � � chain S and resseq 1702 and altloc B</div>
<div>� �}</div>
<div>� }</div>
<div>�}</div>
<div>}</div>
</div>
<div>or enter these selections in appropriate place in
GUI (in one constraint occupancy group).</div>
<div><br>
</div>
<div>Here each selection will get the same occupancy
for all atoms in it, therefore we have both 252
residue and water residue and use altloc B. We don't
have water with altloc A (but you may consider it)
therefore the first selection contains only residue
252. These two selections present in one constrained
group ensures that occupancies of these selections
will add up to 1.</div>
<div><br>
</div>
<div>You can do all the model manipulations in Coot.�<br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>I'll send you corrected pdb file shortly
off-list.</div>
<div><br>
</div>
<div>The useful reading on topic would be</div>
<div><br>
</div>
<div>"13 typical occupancy refinement scenarios and
available options in phenix.refine" by Pavel Afonine
in the latest Computational Crystallography
Newsletter:<br>
</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12"
target="_blank">http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12</a><br>
</div>
<div><br>
</div>
<div>Case #7 is almost your case, the only difference
is one of your residues is water and it has only one
conformation.</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Oleg Sobolev.</div>
</div>
<div class="HOEnZb">
<div class="h5">
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Jan 13, 2016 at
11:59 PM, Helena Taberman <span dir="ltr">
<<a moz-do-not-send="true"
href="mailto:helena.taberman@uef.fi"
target="_blank">helena.taberman@uef.fi</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div style="word-wrap:break-word"><br>
<div>
<div
style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">Hi,</div>
<div
style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><br>
</div>
<div
style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">Thanks
for your advice. It�s still not working.
I use the phenix gui version and if I
set, for example,<br>
<br>
</div>
<div
style="text-align:start;text-indent:0px;word-wrap:break-word">chain
A and resid 249</div>
<div
style="text-align:start;text-indent:0px;word-wrap:break-word">chain
A and resid 252</div>
<div
style="text-align:start;text-indent:0px;word-wrap:break-word">chain
S and resid 1702</div>
<div
style="text-align:start;text-indent:0px;word-wrap:break-word"><br>
</div>
<div
style="text-align:start;text-indent:0px;word-wrap:break-word">as
a constrained group at the occupancy
refinement selections (the two residues
have 2 conformations both and the water
is there just if the conformation of
residue 252 is B) the refinement just
makes the residues a constrained group
alone making even their main chain occ.
something like 0.49 as for the both of
the side chains too. And it also kicks
them a bit out of their densities. So
how to continue? What am I doing wrong?</div>
<div
style="text-align:start;text-indent:0px;word-wrap:break-word"><br>
</div>
<div
style="text-align:start;text-indent:0px;word-wrap:break-word">Best
regards,</div>
<div
style="text-align:start;text-indent:0px;word-wrap:break-word">Helena</div>
</div>
<div>
<div><br>
<div>
<blockquote type="cite">
<div>Folmer Fredslund <<a
moz-do-not-send="true"
href="mailto:folmerf@gmail.com"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:folmerf@gmail.com">folmerf@gmail.com</a></a>>
kirjoitti 11.1.2016 kello 15.20:</div>
<br>
<div>
<div dir="ltr">
<div>
<div>
<div>Hi Helena,<br>
<br>
</div>
I believer this is the
relevant bit from the
manual:<br>
<a moz-do-not-send="true"
href="https://www.phenix-online.org/documentation/reference/refinement.html#occupancy-refinement"
target="_blank">https://www.phenix-online.org/documentation/reference/refinement.html#occupancy-refinement</a>
(in the examples)<br>
<br>
<ol>
<li value="4">
<p>Complex occupancy
refinement strategy
(combination of
various available
occupancy refinement
types):</p>
<pre>% phenix.refine data.hkl model.pdb strategy=occupancies occ.params
</pre>
</li>
</ol>
<p>The amount of atom
selections makes it
inconvenient to type them
all from the command line.
This is why the parameter
file
<tt>occ.params</tt> is
used and it contains
following lines:</p>
<pre>refinement {
refine {
occupancies {
individual = element BR or water
individual = element Zn
constrained_group {
selection = chain A and resseq 1
}
constrained_group {
selection = chain A and resseq 2
selection = chain A and resseq 3
}
constrained_group {
selection = chain X and resname MAN
selection = chain X and resseq 42
selection = chain X and resseq 121
}
remove_selection = chain B and resseq 1 and name O
remove_selection = chain B and resseq 3 and name O
}
}
}
</pre>
<br>
<br>
</div>
Hope this helps,<br>
</div>
Folmer<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">2016-01-11
13:14 GMT+01:00 Christian Roth
<span dir="ltr">
<<a
moz-do-not-send="true"
href="mailto:christianroth034@gmail.com"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:christianroth034@gmail.com">christianroth034@gmail.com</a></a>></span>:<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
<p dir="ltr">Hi Helena, <br>
Indeed you have to group
the relevant aa and the
respective water together
in a constrained group to
avoid your problem and get
the occupancies add up to
1. This us described in
the manual under occupancy
refinement. I can't access
the manual at the moment
to give you a more
detailed answer.</p>
<p dir="ltr">Cheers</p>
<p dir="ltr">Christian</p>
<div class="gmail_quote">
<div>
<div>On 11 Jan 2016
11:56, "Helena
Taberman" <<a
moz-do-not-send="true"
href="mailto:helena.taberman@uef.fi" target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:helena.taberman@uef.fi">helena.taberman@uef.fi</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
style="word-wrap:break-word">Hi,
<div><br>
</div>
<div>I�m trying to
refine a
structure
determined to
1.6 �
resolution.
There�s several
residues with
additional
conformations
and waters with
partial
occupancies
stating that
they would be
there when the
conformation of
the residues
allows it. When
I try to refine
these
conformations
and partially
occupied waters
together the
refinement kicks
the second
conformations
and water
molecules out of
their densities,
since they are
obviously too
close to the
other additional
conformations of
the residues or
the following
residues. What
could I do?
Should I somehow
group them
together or
what?</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Helena</div>
<div><br>
</div>
<div>
<div
style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">Helena
Taberman,
Ph.D.<br>
<br>
University of
Eastern
Finland<br>
Department of
Chemistry<br>
Joensuu Campus<br>
P.O. Box 111<br>
FI-80101
Joensuu,
FINLAND<br>
<br>
Mobile: <a
moz-do-not-send="true"
href="tel:%2B358%2050%20337%202488" value="+358503372488"
target="_blank">
+358 50 337
2488</a><br>
<br>
</div>
</div>
<br>
</div>
<br>
</div>
</div>
_______________________________________________<br>
phenixbb mailing list<br>
<a
moz-do-not-send="true"
href="mailto:phenixbb@phenix-online.org" target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></a><br>
<a
moz-do-not-send="true"
href="http://phenix-online.org/mailman/listinfo/phenixbb"
rel="noreferrer"
target="_blank"><a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a></a><br>
Unsubscribe: <a
moz-do-not-send="true"
href="mailto:phenixbb-leave@phenix-online.org" target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a></a><br>
</blockquote>
</div>
<br>
_______________________________________________<br>
phenixbb mailing list<br>
<a moz-do-not-send="true"
href="mailto:phenixbb@phenix-online.org"
target="_blank">phenixbb@phenix-online.org</a><br>
<a moz-do-not-send="true"
href="http://phenix-online.org/mailman/listinfo/phenixbb"
rel="noreferrer"
target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a
moz-do-not-send="true"
href="mailto:phenixbb-leave@phenix-online.org"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a></a><br>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
<div>Folmer Fredslund<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
<br>
_______________________________________________<br>
phenixbb mailing list<br>
<a moz-do-not-send="true"
href="mailto:phenixbb@phenix-online.org"
target="_blank">phenixbb@phenix-online.org</a><br>
<a moz-do-not-send="true"
href="http://phenix-online.org/mailman/listinfo/phenixbb"
rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a moz-do-not-send="true"
href="mailto:phenixbb-leave@phenix-online.org"
target="_blank">phenixbb-leave@phenix-online.org</a><br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
Unsubscribe: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a></pre>
</blockquote>
<br>
</body>
</html>