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Hi Qing,<br>
<br>
As you observed, different programs report different correlation
values. You can get any correlation value you want by changing the
region over which the correlation is computed, or the formula for
the correlation, or the resolution of the simulated map. <br>
<br>
First Chimera 1.5 or newer reports two correlation values: the
correlation about the mean and the correlation about 0. It is
typical for EM maps to report the correlation about zero which is
usually much higher. If you use the old Chimera 1.4 it only reports
the lower correlation about mean. Formulas for these two
correlation values are given in the Chimera manual.<br>
<br>
Next you need to choose the region over which the correlation is
calculated. Your approach of setting the simulated map contour
level so the enclosed volume is what is expected is good. Make sure
you list the simulated map first in the measure correlation command
since the first volume determines the region for the computation.<br>
<br>
Lastly, the simulated map resolution should match the map
resolution. There are different definitions of resolution used by
the EM community -- it is controversial. In any case you want the
simulated map to match the level of detail seen in the experimental
map. If it doesn't match then you will get lower correlation. You
may need to try a range of resolutions. The molmap documentation
describes the different options for how the resolution value is used
to make the simulated map.<br>
<br>
Unfortunately reported correlation values in publications rarely
describe all the above choices so the values are not very meaningful
or reproducible.<br>
<br>
Tom<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] CC calculation<br>
From: Qing Xie<br>
To: Tom Goddard <br>
Date: 1/26/12 11:31 AM<br>
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<div>Hi, Tom,</div>
<div><font face="tahoma">Thanks for your help!</font></div>
<div><font face="tahoma">I'm helping to model a structure (.pdb)
into a EM density map.... This is my first time using
Chimera. I got a CC of ~0.87 after refining the structure
against the EM map using Rsref in CNS. I was suggested to
cross-check the CC by using Chimera since Chimera is more
popular in EM community.</font></div>
<div> </div>
<div><font face="tahoma">I calculated the simulated map
following your email, but the CC varies a lot by choosing
different contour level for the EM map (#0). The EM map's
range is from -0.12 to 0.17 (sigma 0.013), while the
simulated map's range is from 0 to 2.64 (sigma 0.20). After
I tried to claculate the volumes and then matchs the volume
of (#0) to (#1), CC is only ~0.63.</font></div>
<div> </div>
<div><font face="tahoma">I also tried CCP4 overlapmap and it
gave me a CC of ~0.73.</font></div>
<div> </div>
<div><font face="tahoma">Do you have any other suggestions?</font></div>
<div> </div>
<div><font face="tahoma">Thank you very much!</font></div>
<div> </div>
<div><font face="tahoma">Qing</font></div>
<br>
</div>
</blockquote>
<br>
<br>
<br>
Tom Goddard wrote:
<blockquote cite="mid:4F1E0D10.2000408@sonic.net" type="cite">
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If the PDB (#1) is already fit to the map (#0) you could create a
simulated map for the pdb then measure its correlation with the
experimental map:<br>
<br>
molmap #1 12.5<br>
measure correlation #2 #1<br>
<br>
The 12.5 in the molmap command is the resolution for the simulated
map which should match the experimental map. By default the
correlation will be measured within the displayed contour level of
the first map given in the command.<br>
<br>
The commands are described in the Chimera User's Guide.<br>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html</a><br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#correlation">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#correlation</a><br>
<br>
Tom<br>
<br>
<br>
<br>
<br>
<blockquote
cite="mid:F912366B3340F54EAD33D9C1E36518E10B0F569177@EX-MB07.ohsu.edu"
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<div dir="ltr"><font color="#000000" face="Tahoma" size="2">Hi,</font></div>
<div dir="ltr"><font face="tahoma">Can anyone help me with
calculating correlation coefficient from a .pdb model to a
.mrc map?</font></div>
<div dir="ltr"> </div>
<div dir="ltr"><font face="tahoma">Thank you!</font></div>
<div dir="ltr"> </div>
<div dir="ltr"><font face="tahoma">Qing</font></div>
</div>
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