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Hi Emilia,<br>
<br>
<blockquote type="cite"
cite="mid:CAHB=7XgnnwoAANHYHQP83+6hsE5uZc8eJO2eJzSqX==eM3SR4Q@mail.gmail.com">
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<div dir="ltr"><span class="gmail-s1" style="font-kerning:none">For
relatively low resolution maps, where sugar moieties cannot be
placed unambiguously, in theory (say Agirre<span
class="gmail-Apple-converted-space"> </span>(2017) and
Emsley and Crispin (2018)) pyranose placement within the map
should be quite highly restrained by ideal geometry for the
specific sugar expected from prior knowledge. In practice,
however, it’s not entirely clear how to maintain these
restraints on pyranose geometry and conformation during manual
building in Coot, (....) </span></div>
</blockquote>
<br>
I will skip part about Coot as I saw you got some good advice on
ccp4bb from Paul but I'll say something re refinement in Phenix..<br>
<br>
<blockquote type="cite"
cite="mid:CAHB=7XgnnwoAANHYHQP83+6hsE5uZc8eJO2eJzSqX==eM3SR4Q@mail.gmail.com">
<div dir="ltr"><span class="gmail-s1" style="font-kerning:none">Meanwhile,
in Phenix I don’t do anything specific for the refinement of
glycosylation sugars (should I?) other than apply the
appropriate restraints for any low resolution EM map; are
there specific restraints files I ought to be using within
Phenix real space refine jobs for N-linked sugars?</span></div>
</blockquote>
<br>
Normally, you don't really need to do anything special. If input
geometry is meaningful then everything should be linked correctly
and refined fine as well. So.. is this the case?<br>
<br>
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cite="mid:CAHB=7XgnnwoAANHYHQP83+6hsE5uZc8eJO2eJzSqX==eM3SR4Q@mail.gmail.com">
<div dir="ltr">
<span class="gmail-s1" style="font-kerning:none">Then I noticed
that loads of existing PDB entries containing N-linked glycans
contain similar outliers in pyranose geometry. </span></div>
</blockquote>
<br>
Deposited models in PDB are not problems free as was documented by
others many times in the past. So what you observe isn't too
surprising.<br>
<br>
<blockquote type="cite"
cite="mid:CAHB=7XgnnwoAANHYHQP83+6hsE5uZc8eJO2eJzSqX==eM3SR4Q@mail.gmail.com">
<div dir="ltr"><span class="gmail-s1" style="font-kerning:none">Or
is this a tolerable situation where sugar geometries differ
from ideal even at low resolution? </span></div>
</blockquote>
<br>
Refinement uses restraints on covalent geometry, not constraints. So
deviations from idea library values are expected. The higher the
resolution, the larger deviations can be tolerable. The lower the
resolution, the model idealized geometry is expected.<br>
<br>
<blockquote type="cite"
cite="mid:CAHB=7XgnnwoAANHYHQP83+6hsE5uZc8eJO2eJzSqX==eM3SR4Q@mail.gmail.com">
<div dir="ltr"><span class="gmail-s1" style="font-kerning:none">Is
it perhaps a matter of different targets being used for PDB
validation by the rcsb versus by Coot?</span></div>
</blockquote>
<br>
This is a valid point and may well be the case!<br>
<br>
Feel free to send me inputs and outputs and indicate what exactly
you find problematic or just worrisome and I will check. Otherwise
it's hard to discuss this without looking at specific example.<br>
<br>
All the best,<br>
Pavel<br>
<br>
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