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<p>Hi Oleg,</p>
<p>I'm also curious why for the same amount of residues 8101 two
numbers for 'whole' and 'loop' are different?</p>
<p>Pavel<br>
</p>
<div class="moz-cite-prefix">On 10/15/21 09:16, Oleg Sobolev wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CADd3otGU7xp2CKYt7krPvmqcY0-YDGFC2MOecx4+-JO1hz-JLA@mail.gmail.com">
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<div dir="ltr">Hello Hannah,
<div><br>
</div>
<div>I'm glad to investigate if you send me the model file
(off-list). It would also help if you could specify the Phenix
version you are using. The only thing that is coming to my
mind without looking at the file is that our procedure for
secondary structure assignment is not finding any SS elements
in your 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 Fri, Oct 15, 2021 at 5:54
AM Hannah Bridges <<a href="mailto:hrb@mrc-mbu.cam.ac.uk"
moz-do-not-send="true" class="moz-txt-link-freetext">hrb@mrc-mbu.cam.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">
<div>
<p>Hello, <br>
</p>
<p>I have a PDB for which, when I run either realspace
refinement or validation, phenix does not show rama-z
scores for helix or sheet (and the structure is not
entirely loops..)<br>
</p>
<p>Rama-Z (Ramachandran plot Z-score):<br>
Interpretation: bad |Rama-Z| > 3; suspicious 2 <
|Rama-Z| < 3; good |Rama-Z| < 2.<br>
Scores for whole/helix/sheet/loop are scaled
independently;<br>
therefore, the values are not related in a simple
manner.<br>
whole: -0.68 (0.08), residues: 8101<br>
helix: None (None), residues: 0<br>
sheet: None (None), residues: 0<br>
loop : -0.50 (0.06), residues: 8101<br>
</p>
<p>It seems peculiar to this one model, as other very
similar ones are fine, but is this something that other
people have seen before? I can supply the PBD off-list for
investigation.</p>
<p>Best wishes</p>
<p>Hannah<br>
</p>
<pre cols="72">--
Dr Hannah Bridges
Investigator Scientist
MRC Mitochondrial Biology Unit
The Keith Peters Building
University of Cambridge
Cambridge Biomedical Campus
Hills Road
Cambridge
CB2 0XY
United Kingdom
Telephone : 01223 252812</pre>
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