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<p>Thanks for the reply, Ashley, Claus, Gerard and Clemens.</p>
<p>The nominal resolution is 3.35Å but its is a large structure
consisting of a dimer of >1,100 residues arranged as seven
domains in tandem. <br>
</p>
<p>This makes the overall structure quite flexible and poorly
defined for some domains. <br>
</p>
<p>We got initial phases to 4Å from a selenomethione-SAD experiment,
which we could extend to 3.35Å.</p>
<p>The model is essentially ready and we are struggling with the
final steps of refinement. Unfortunately, we do not have any
reference model, it's a</p>
<p>new structure, and after each manual rebuilding step and fixing
of small geometric inconsistencies, subsequent refinement creates
another region</p>
<p>that needs to be fixed, and so on.<br>
</p>
<p>Buster performs very nicely, as usual, it is our program of
choice for final refinement steps and map calculation. It is just
that, for these particular</p>
<p>cases of low resolution, poorly defined stretches, missing
density for side chains, etc., it would be very interesting to
have an option to restrain <br>
</p>
<p>rotamers and main-chain angles to acceptable values to get the
best model possible given these limitations. I guess this should
be even more actual</p>
<p>for cryo-EM, are there any plans to adapt BUSTER to such maps?<br>
</p>
<p>Having said all this, we will try with the parameters you mention
and with STARANISO.</p>
<p>Thanks a lot and best regards,</p>
<p>Xavier<br>
</p>
<br>
<div class="moz-cite-prefix">On 7/2/18 15:32, Ashley Pike wrote:<br>
</div>
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cite="mid:96D4B2775AB2BB499763EA2F174A0D7622FE7D1F@MBX06.ad.oak.ox.ac.uk">
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<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Xavier,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">No
– buster doesn’t have any explicit rotamer/rama restraints
as far as I know. In my experience refining in the 3.4-4A
range, the best way to achieve such restraints is to use
target restraints to a reference model(s). If this doesn’t
exist then it will be challenging. What is the resolution
you are working at? Also what is the level of anisotropy –
if it is anything like most of our ‘low resolution’ data,
the headline number often hides even lower resolution in
certain directions! Having said this, if you have a
goodish input model then buster normally does a really good
job of keeping everything together nicely.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">There
are a lot of individual geometry parameters you could try
tinkering with:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><a
href="https://www.globalphasing.com/buster/manual/autobuster/manual/appendix1.html#SetvarParameter_GeometryWeight_names"
moz-do-not-send="true">https://www.globalphasing.com/buster/manual/autobuster/manual/appendix1.html#SetvarParameter_GeometryWeight_names</a><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Globally
you can define a rmsd bond target using –r option<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Ashley<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"
lang="EN-US">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"
lang="EN-US"> buster-discuss
[<a class="moz-txt-link-freetext" href="mailto:buster-discuss-bounces@globalphasing.com">mailto:buster-discuss-bounces@globalphasing.com</a>]
<b>On Behalf Of </b>F.Xavier Gomis-Rüth<br>
<b>Sent:</b> 07 February 2018 11:36<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:buster-discuss@globalphasing.com">buster-discuss@globalphasing.com</a><br>
<b>Subject:</b> [buster-discuss] Restraints<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p>Dear Buster List,<o:p></o:p></p>
<p>we are currently working with a very large low-resolution
structure and using BUSTER/TNT for refinement and map
calculation.<o:p></o:p></p>
<p>Given the limitation of the resolution, we would be very
interested in applying enhanced rotamer, geometric (for bond
lengths and<o:p></o:p></p>
<p>angles) and Ramachandran restraints, as the evaluation with
MOLPROBITY after each refinement cycle gives a very high
number of<o:p></o:p></p>
<p>outliers despite a good overall Clashscore (6.14; 100%) and
Molprobity Score (2.63; 96%). Is there a way to impose such
restraints?<o:p></o:p></p>
<p>Thanks a lot in advance,<o:p></o:p></p>
<p class="MsoNormal">Xavier <o:p></o:p></p>
<div>
<p class="MsoNormal">-- <br>
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src="cid:part2.018504E3.4783FB40@ibmb.csic.es" class=""
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</blockquote>
<br>
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