<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">ashley.pike@sgc.ox.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Oleg,<u></u><u></u></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.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Many thanks,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Ashley<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif">From:</span></b><span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif"> Oleg Sobolev <<a href="mailto:osobolev@lbl.gov" target="_blank">osobolev@lbl.gov</a>>
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<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">ashley.pike@sgc.ox.ac.uk</a>><br>
<b>Cc:</b> <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> Re: [phenixbb] Rotamer restraints in phenix.real_space_refine<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Hi Ashley,<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<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.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">I can have a closer look if you send me the .log file (off-list).<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Best regards,<u></u><u></u></p>
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<p class="MsoNormal">Oleg Sobolev.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<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">ashley.pike@sgc.ox.ac.uk</a>> wrote:<u></u><u></u></p>
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<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.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></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.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Many thanks,<u></u><u></u></p>
<p class="MsoNormal">Ashley<u></u><u></u></p>
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