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<p>Dear Ashley,</p>
<p><br>
</p>
<p>Thank you for bringing this issue to our attention. We appreciate
getting feedback / problem reports from users so we can ensure we
continue to improve our software.</p>
<p><br>
</p>
<p>Your findings are a little unexpected but we have occasionally
had reports about similar behaviour before.<br>
</p>
<p>Firstly, it is not at all surprising that you get behaviour
closer to your expectation from a restraint dictionary from Grade
using the -bigplanes options. By default, Grade generates a
series of overlapping 4-atom plane restraints (as you will see if
you look at the standard Grade UD1 dictionary). There is also a
good reason for doing it this way, since some (large) ring systems
actually show real deviation from exact planarity (e.g. FAD) and
by using a collection of small, overlapping planes we can handle
this. Usually, this approach is quite sufficient to maintain
planarity in rings. However, not always. The -bigplanes option
sees overlapped 4-atom planes conflated (where appropriate) into a
single, large plane. In this case, if you look at the bigplanes
dictionary you will see a single plane restraint for the uracyl
ring, including C1.</p>
<p><br>
</p>
<p>We have tried running BUSTER, with UD1 dictionaries generated a)
with Grade, b) with Grade and -bigplanes and c) by CCP4, on a
number of PDB structures that contain UD1 and thus far we have
been unable to reproduce your problem. Indeed, in one of the
models we looked at, 4gx5 (a 3.1A structure) the uracyl ring is
non-planar in the deposited model but ends up completely planar
after BUSTER (regardless of which dictionary I use).</p>
<p><br>
</p>
<p>The suggestion made to you by Marco Bellinzoni may well work but
it is an approach that we would urge caution against using, at
least at this stage.</p>
<p>We wonder if there is a more particular issue with the local
environment around the UD1 that results in the C1 being forced out
of plane of the uracyl ring? If the cause is some modelling
problem, Marco's suggestion may lead to the planarity being
maintained but may simply mask the root cause. His suggestion will
also apply globally over the whole structure, not locally on the
UD1.</p>
<p><br>
</p>
<p>What is the environment around the UD1? Are there any close
contacts / residues that need to be resolved? What about alternate
conformations?<br>
</p>
<p><br>
</p>
<p>Also, and despite the resolution, is your model (or just the
UD1) hydrogenated - this may also have also have an impact on the
refinement. Note that BUSTER does not use a "riding hydrogen"
model as refmac does, it includes them in calculation of the
geometric terms, so these could well be having an impact.</p>
<p><br>
</p>
<p>Would it also be possible for you to send us the model / mtz file
so we can look at this directly.</p>
<p><br>
</p>
<p>Best wishes</p>
<p><br>
</p>
<p>Andrew and Clemens<br>
</p>
<br>
<div class="moz-cite-prefix">On 31/01/18 14:41, Ashley Pike wrote:<br>
</div>
<blockquote type="cite"
cite="mid:96D4B2775AB2BB499763EA2F174A0D7622FE5470@MBX06.ad.oak.ox.ac.uk">
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<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal">Does anyone have any tips to force buster
to maintain planarity when refining ligands. I am refining a
UDP-GlcNAc (UD1) and the N1 of the uracyl base is refining out
of plane. Using the bigplanes option when generating the cif
helps a lot but the N atom is approx. 0.1A out of the plane
(compared to ideal or refmac refined). N1 is in same plane as
aromatic ring but not with C1 of ribose. How to I increase
weighting towards geometry for ligand – perhaps adding
something to gelly file to modify overall weight?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Using the latest snapshot version of buster<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Resolution is 3.1A so perhaps I can’t
expect anything better.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">FWIW the cif file used was generated by
grade from the PDB ligand entry. The cif file itself is fine
as using to refine in coot or refmac results in maintenance of
planarity.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Cheers,<o:p></o:p></p>
<p class="MsoNormal">Ashley<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Lower buster-refined model shows N1 of
uracyl ring out-of-plane wrt to C1 atom of sugar on left-hand
side (top models are coot-idealised and refmac-refined)<o:p></o:p></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB"><img
id="Picture_x0020_1"
src="cid:part1.BEB35280.2222C89C@globalphasing.com"
class="" height="218" width="849"></span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">--<o:p></o:p></p>
<p class="MsoNormal">Dr. Ashley Pike<o:p></o:p></p>
<p class="MsoNormal">Membrane Protein Crystallography |
Structural Genomics Consortium | University of Oxford<o:p></o:p></p>
</div>
<br>
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<br>
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<br>
<div class="moz-signature">-- <br>
<div class="moz-signature">
<title></title>
----------------------------------------------------------<br>
<b><font color="#3333ff">Dr. Andrew J. Sharff </font><font
color="#3333ff">D.Phil</font></b><b><font color="#3333ff"><br>
</font></b><font color="#3333ff"><font color="#000000">Research
Scientist / Software Developer<br>
Global Phasing Ltd<br>
Sheraton House<br>
Castle Park<br>
Cambridge CB3 0AX<br>
UK<br>
Tel: +(0)1223 353033<br>
Fax: +(0)1223 366889<br>
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