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Hi Katherine,<br>
<br>
you can take RMSD from PDB file header, example:<br>
<br>
REMARK Final: r_work = 0.1588 r_free = 0.1773 <b>bonds = 0.015
angles = 1.221</b><br>
<br>
or if you scroll down some more:<br>
<br>
REMARK�� 3� DEVIATIONS FROM IDEAL VALUES.<br>
REMARK�� 3���������������� RMSD���� MAX� COUNT<br>
<b>REMARK�� 3�� BOND����� :� 0.015�� 0.620�� 4192</b><b><br>
</b><b>REMARK�� 3�� ANGLE���� :� 1.221�� 7.451�� 5663</b><b><br>
</b><br>
or from phenix.refine log file. <br>
<br>
Also you can just calculate them from PDB file:<br>
<br>
phenix.pdbtools model.pdb model_stat=true<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 8/25/14 2:25 PM, Katherine Sippel
wrote:<br>
</div>
<blockquote
cite="mid:CAPpRgj0tofq+9ozGZmtytn503DAY4RwLjkLNPJaqyQweby=C4Q@mail.gmail.com"
type="cite">
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<div>
<div>Hi all,<br>
<br>
</div>
I was trying to prep a structure for PDB deposition. All the
protein atoms were good, but I needed to correct some ADP and
ligand issues. I ran coordinate refinement only on the ligands
and subsequent ADP refinement. Everything was good, except the
RSMD values output are clearly only for the ligands. Now I am
wondering which values in the header I can trust as far as
deposition goes. I tried to do a workaround where I ran refine
with 0 macrocycles to see if I could get the proper values,
but obviously the bulk solvent is different and I get higher R
values. <br>
<br>
I am wondering if I can run validation to get the correct RMSD
values or if there are other header values that might have
been affected by not refining all the coordinates?<br>
<br>
</div>
Cheers,<br>
Katherine<br clear="all">
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<div><br>
-- <br>
<div dir="ltr">"Nil illegitimo carborundum"<i> -
</i>Didactylos</div>
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