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Tue Sep 25 15:04:34 PDT 2012


a><br>
Date : 07/07/2014 - 11:47 (GMTDT)<br>
To : <a href=3D"mailto:phenixbb at phenix-online.org">phenixbb at phenix-online.o=
rg</a><br>
<div class=3D"im HOEnZb">Subject : Re: [phenixbb] alternatives to RMSD<br>
<br>
</div><div class=3D"HOEnZb"><div class=3D"h5">Hi Patrick,<br>
<br>
why don&#39;t you superimpose only the matching segments and report their<b=
r>
RMSD? It is the common procedure for RMSD&#39;s from superpositions to<br>
report the aligned residues together with the RMSD.<br>
<br>
The advantage compared to a map CC is similar to that of R_sym over<br>
R_meas: readers have a better concept (from experience) of what the<br>
numbers mean.<br>
<br>
Best,<br>
Tim<br>
<br>
On 07/02/2014 05:15 PM, Patrick. C wrote:<br>
&gt; Hi Phenix users,<br>
&gt;<br>
&gt; I am not a crystallographer but I though you guys might be a good plac=
e to ask<br>
&gt; this question.<br>
&gt;<br>
&gt; I have 2 super secondary structures, A and B and they consist of Helix=
-turn-Strand<br>
&gt;<br>
&gt; Due to the turn the two structures have a poor RMSD because the two fl=
anking<br>
&gt; fragments of Helix and Strand are far from each other but when I super=
impose the<br>
&gt; two fragments individually(helixA with helix B and standA with strandB=
 in Pymol<br>
&gt; they align very well).<br>
&gt;<br>
&gt; Now, is there a way to express this instead of using the RMSD?<br>
&gt; When the two structures align well the RMSD is very good but a slight =
movement<br>
&gt; and the RMSD is awful.<br>
&gt; But looking at the two structures I can see they follow the same path =
through space.<br>
&gt;<br>
&gt; Thank you,<br>
&gt; Patrick<br>
&gt;<br>
&gt;<br>
&gt; ----------------------------------------------------------------------=
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&gt;<br>
&gt;<br>
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&gt;<br>
<br>
--<br>
Dr Tim Gruene<br>
Institut fuer anorganische Chemie<br>
Tammannstr. 4<br>
D-37077 Goettingen<br>
<br>
GPG Key ID =3D A46BEE1A<br>
<br>
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</div></div></blockquote></div><br><br clear=3D"all"><div><br></div>-- <br>=
Morten K Gr=C3=B8ftehauge, PhD=C2=A0<div>Pohl Group</div><div>Durham Univer=
sity</div>
</div>

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