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Hi Rakesh,<br>
<br>
Chimera Fit in Map and also the measure correlation command by
default only compute the cross-correlation within the displayed
envelope of the first map. So it should give the masked value you
are looking for, although the actual value will depend sensitively
on the surface level of the first map that you choose since that
will control which grid points near the boundary of your fragment
are included. There is no right answer about how tightly to mask
and since the correlation value is so sensitive to that it is not
too meaningful to try to compare correlation values although people
do it anyways.<br>
<br>
Check out the measure correlation and fit in map docs for more
details<br>
<br>
<a class="moz-txt-link-freetext" href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlation">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlation</a><br>
<br>
<a class="moz-txt-link-freetext" href="https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html">https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html</a><br>
<br>
Tom<br>
<br>
<br>
<div class="moz-cite-prefix">On 12/6/2021 5:09 PM, Rakesh
Ramachandran wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CADZzdKYwmXNgdZ1i1Jfhk8yec6vXrtBghiT_t+qeQPv0fSL7Og@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Sorry, what I meant was say I am fitting a
fragment into a large map, the cross correlation should be
calculated only around the fitted region of the fragment, that
is any voxels outside the fragment location should not be taken
into account in the cross-correlation score.
<div><br>
</div>
<div>I need this because I am fitting fragments of different
sizes into a map and I tend to get quite similar cross
correlation scores even though principally it should.</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Dec 6, 2021 at 5:03 PM
Tom Goddard <<a href="mailto:goddard@sonic.net"
moz-do-not-send="true">goddard@sonic.net</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div> Hi Rakesh,<br>
<br>
I don't understand what you mean by "length normalized by
masking". Chimera can compute cross-correlation using the
Fit in Map panel. If you are fitting an atomic model to the
map it needs to simulate a map from the atomic model since
correlation is between two maps. You do that using the "Use
map simulated from atoms" option in the Fit in Map panel
Options pane.<br>
<br>
Tom<br>
<br>
<br>
<div>On 12/6/2021 4:00 PM, Rakesh Ramachandran wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Tom,
<div> </div>
<div> I am using Chimera Fit in Map for EM fitting.
Though it does fit well, I want to calculate a cross
correlation score based on the model map size, that is
the cross correlation should be length normalized by
masking the rest of the map.<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">
<div dir="ltr">Regards<br>
Rakesh Ramachandran<br>
</div>
</div>
</div>
</div>
</blockquote>
<br>
</div>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr" class="gmail_signature">
<div dir="ltr">Regards<br>
Rakesh Ramachandran<br>
</div>
</div>
</blockquote>
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