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Hi Patrick,<br>
supposing models are superposed appropriately (see previous comments
on phenixbb), step-by-step I see it as following:<br>
- compute density map for model A (or its Fourier synthesis of
resolution 1A or higher),<br>
- compute density map for model B (or its Fourier synthesis of
resolution 1A or higher),<br>
- compute map CC per residue or per atom between maps corresponding
to A and B.<br>
<br>
I would think that "superposed appropriately" is a key here.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 7/5/14, 7:22 AM, PC wrote:<br>
</div>
<blockquote cite="mid:630B0B7DEDE.0000092Bpatrick.cossins@inbox.com"
type="cite">
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<div>Hi Pavel,</div>
<div><br>
</div>
<div>Thank you very much, this sounds very interesting.</div>
<div><br>
</div>
<div>I have used ccp4, coot and phenix but I am no expert but I am
definitely interested in trying this method if you could give
more information.</div>
<div><br>
</div>
<div>Thank you,</div>
<div>Patrick. </div>
<br>
<br>
<blockquote style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px;
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<div class="msgHeaders">-----Original Message-----<br>
<b>From:</b> <a class="moz-txt-link-abbreviated" href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a><br>
<b>Sent:</b> Fri, 04 Jul 2014 20:34:33 -0700<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:patrick.cossins@inbox.com">patrick.cossins@inbox.com</a>,
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> Re: [phenixbb] alternatives to RMSD<br>
<br>
</div>
<div class="oldBody">
<div> 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>
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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>
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<br>
</div>
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