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Hi Ashley,<br>
<br>
yes, the behavior is different now. Before we would restrain each
residue to its nearest valid rotamer without considering density
map, which works well in many cases but doesn't in some. In current
version we optimize rotamers to minimize clashes (but we mind
H-bonds) and maximize model-to-map fit. Clearly, it may happen that
local model geometry is such that no optimal fit is possible, this
is probably responsible for some outliers that remain after
refinement.<br>
<br>
If you have a clear example where this does no work please send it
to us and we will investigate.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 2/28/19 09:59, Oleg Sobolev wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CADd3otGNJ3YtDBnipNpEARvxzCMnL4==Oh=QZe2tiaXDwRyMaQ@mail.gmail.com">
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<div dir="ltr">Hi Ashley,
<div><br>
</div>
<div>Indeed, apart from strategy defaults, the rotamer fitting
algorithm itself was changed between 1.13 and 1.14. It is
possible it behaves slightly different (we were hoping for the
better behavior in most cases). I'm not sure that it is
possible to get exact 1.13 behavior in 1.14. I would expect
you get small amount of rotamer outliers (<1%). Otherwise
we probably should investigate. Sometimes inclusion of
hydrogen atoms could help get a better refined model.</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Oleg Sobolev. </div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Feb 28, 2019 at 4:24
AM Ashley Pike <<a href="mailto:ashley.pike@sgc.ox.ac.uk"
moz-do-not-send="true">ashley.pike@sgc.ox.ac.uk</a>>
wrote:<br>
</div>
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0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<div class="gmail-m_-5657445803015181633WordSection1">
<p class="MsoNormal"><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Oleg,</span></p>
<p class="MsoNormal"><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Thanks
- so behaviour has changed. Running with local_grid +
rotamer restraints=true seems to optimise rotamers
(although does not necessarily eliminate outliers). Is
there an equivalent combination that enforces rotamers
(ie. doesn’t allow outliers)? This is behaviour of
1.13 with just rotamer_restraints=true (and no
local_grid _search). In my case, I can't really
justify having rotamer outliers when refining against
4A cryo-em maps.</span></p>
<p class="MsoNormal"><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Many
thanks,</span></p>
<p class="MsoNormal"><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Ashley</span></p>
<p class="MsoNormal"><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span></p>
<p class="MsoNormal"><b><span
style="font-size:11pt;font-family:Calibri,sans-serif"
lang="EN-US">From:</span></b><span
style="font-size:11pt;font-family:Calibri,sans-serif"
lang="EN-US"> Oleg Sobolev <<a
href="mailto:osobolev@lbl.gov" target="_blank"
moz-do-not-send="true">osobolev@lbl.gov</a>>
<br>
<b>Sent:</b> 28 February 2019 00:14<br>
<b>To:</b> Ashley Pike <<a
href="mailto:ashley.pike@sgc.ox.ac.uk"
target="_blank" moz-do-not-send="true">ashley.pike@sgc.ox.ac.uk</a>><br>
<b>Cc:</b> <a
href="mailto:phenixbb@phenix-online.org"
target="_blank" moz-do-not-send="true">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> Re: [phenixbb] Rotamer restraints in
phenix.real_space_refine</span></p>
<p class="MsoNormal"> </p>
<div>
<p class="MsoNormal">Hi Ashley,</p>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Do you have "local_grid_search"
box checked in refinement settings->strategy when
running 1.14? This should be on by default since
1.14, but it was not the case in 1.13. Sometimes
people using .eff files from 1.13 in later versions
end up without old defaults for refinement strategy,
disabling rotamer fitting.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">I can have a closer look if you
send me the .log file (off-list).</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Best regards,</p>
</div>
<div>
<p class="MsoNormal">Oleg Sobolev.</p>
</div>
</div>
<p class="MsoNormal"> </p>
<div>
<div>
<p class="MsoNormal">On Wed, Feb 27, 2019 at 10:56 AM
Ashley Pike <<a
href="mailto:ashley.pike@sgc.ox.ac.uk"
target="_blank" moz-do-not-send="true">ashley.pike@sgc.ox.ac.uk</a>>
wrote:</p>
</div>
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solid rgb(204,204,204);padding:0cm 0cm 0cm
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<div>
<p class="MsoNormal">Hi - Am I right in thinking
that rotamer restraints behaves differently in
latest official release (1.14-3260) compared to
last but one official release (1.13-2998)?
Issuing rotamer_restraints=True from command
line or GUI used to give 0% rotamer outliers in
the molprobity analysis at end of log in
1.13-2998 but now in 1.14 gives non-zero for
same input model. It is as if they are not being
applied.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">In the old log file it used
to clearly print - **Update rotamer
restraints*** after every macrocycle, in the
1.14 logs this is omitted.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Many thanks,</p>
<p class="MsoNormal">Ashley</p>
</div>
</div>
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