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Hi Patrick,<br>
<br>
RMSD is a poor measure in this case as it does not account for
B-factors, occupancies, alternative conformations and so on
information a crystal structure model may make available.
Macromolecules are not a bunch of points in space.<br>
<br>
While I'm sure more thorough methods exist, I would vote for the
simplest, most direct and obvious one. You can calculate electron
density map using a Gaussian approximation from model A and B (yes,
electron density map - not a Fourier image of it!). That will
naturally account for all: B-factors, occupancies, other disorder.
Then you can calculate a map similarity measure, such as map
correlation, for instance. After all, why use a cannon to kill a
fly?!<br>
<br>
If you are interested to follow this route I can explain the
details.<br>
<br>
All the best,<br>
Pavel<br>
<br>
<blockquote cite="mid:3DC97382C23.000010FBpatrick.cossins@inbox.com"
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Hi Phenix users,
<div><br>
</div>
<div>I am not a crystallographer but I though you guys might be a
good place to ask this question.</div>
<div><br>
</div>
<div>I have 2 super secondary structures, A and B and they consist
of Helix-turn-Strand</div>
<div><br>
</div>
<div>Due to the turn the two structures have a poor RMSD because
the two flanking fragments of Helix and Strand are far from each
other but when I superimpose the two fragments
individually(helixA with helix B and standA with strandB in
Pymol they align very well).</div>
<div><br>
</div>
<div>Now, is there a way to express this instead of using the
RMSD?</div>
<div>When the two structures align well the RMSD is very good but
a slight movement and the RMSD is awful.</div>
<div>But looking at the two structures I can see they follow the
same path through space.</div>
<div><br>
</div>
<div>Thank you,</div>
<div>Patrick<br>
</div>
</blockquote>
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