<div dir="ltr">If the RMS of angles are so deviant and the structure is high resolution then wouldn't it show up in COOT density fitting?</div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Sep 19, 2014 at 12:50 PM, Katherine Sippel <span dir="ltr"><<a href="mailto:katherine.sippel@gmail.com" target="_blank">katherine.sippel@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>This is from Phenix's FAQ page...<br><br><strong>"My resolution is X Angstroms; what should RMS(bonds) and RMS(angles) be?</strong>
<br><br><a name="1488ed313d62fff6_anch30"></a>
This is somewhat controversial, but absolute upper limits for a well-refined
protein structure at high resolution are typically 0.02 for RMS(bonds) and
2.0 for RMS(angles); usually they will be significantly lower. As resolution
decreases the acceptable deviation from geometry restraints also decreases,
so at 3.5 Angstrom, more appropriate values would be 0.01 and 1.0." <br><br></div>If the histogram shows that the RMS(angles) average higher than 2 then I think that would be a result of poorly refined structures skewing the graph rather than a reflection of what the RMS should be. <br><br><br></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Fri, Sep 19, 2014 at 1:57 AM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
<div bgcolor="#FFFFFF" text="#000000">
Hi,<br>
<br>
if you make sure these values are not caused by a handful of atoms
that flew a distance apart for whatever reason then values like ok
to me. This is why looking at a histogram of deviations (bond,
angles etc) is way more useful than looking at just one number!<br>
<br>
Pavel<br>
<br>
<br>
<div>On 9/18/14 1:32 PM, C wrote:<br>
</div>
<blockquote type="cite">
Hi,
<div><br>
</div>
<div>Refining using phenix I find the RMS angle drifting towards
2.3-2.7 range when validating the resulting structure.</div>
<div><br>
</div>
<div>These are high resolution structures and I was wondering if
someone could comment on whether 2.3-2.7 values are worrisome?</div>
<div>Thank you</div>
<br>
</blockquote>
<br>
</div>
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