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Hi Bala,<br>
<br>
One idea is to set the density map contour level so that the
surface encloses the expected volume for the molecular assembly. An
example of that is in a Chimera tutorial<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.cgl.ucsf.edu/chimera/data/tutorials/eman07/chimera-eman-2007.html#part2">http://www.cgl.ucsf.edu/chimera/data/tutorials/eman07/chimera-eman-2007.html#part2</a><br>
<br>
Just the data inside the contour level is used for computing
correlation coefficients in Chimera (unless "use only data above
contour level..." option is turned off). So the contour level has a
big effect on the fit correlation coefficients, for example it might
vary from 0.5 for a low contour level to 0.9 for a high contour
level. It doesn't mean the fits are any different -- they could be
in identical positions. But the data used for calculating the
correlation is different. People rarely talk about this but
basically you can get any correlation value you want. Which contour
level is best. There is no obvious answer to that. But the
suggestion above to use the level to enclose the right volume is
sensible to try.<br>
<br>
Tom<br>
<br>
<br>
<blockquote
cite="mid:CA+WPOVOTJ8nepOsqWyeCNa8WgGnYjMC3Kv--nntcEwNnuDdp4Q@mail.gmail.com"
type="cite">Hi Elaine,<br>
<br>
Thank you. <br>
<br>
I wanted to ask about choosing an optimal threshold level of the
volume data (the experimental map) instead of which i wrote as
resolution of the volume data. I admit that i have not mentioned
it clearly in the previous mail. <br>
<br>
I tried to fit a structure on to a map and i found that the
correlation value, Avg and Inside in the fit-list changes
depending up on the threshold level of the volume data i chose. So
i am not getting how to choose a correct threshold value of the
volume data. <br>
<br>
Cheers,<br>
Bala<br>
<br>
<br>
<div class="gmail_quote">On Wed, Mar 7, 2012 at 7:01 PM, Elaine
Meng <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Bala,<br>
Since you can't control the resolution of the experimental
density map, I'm guessing you mean what resolution value to
use for the map simulated from the atoms that are being fit
into the map (simulating a second map allows scoring the fit
by map-map correlation).<br>
<br>
I believe you would want to use the same or similar value to
the experimental map's resolution. In turn, that value should
be available from the database where you got the map and/or
the publication describing the map (or if not publicly
available, the scientists who did the experiment).<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<div class="HOEnZb">
<div class="h5"><br>
<br>
On Mar 7, 2012, at 3:22 AM, Bala subramanian wrote:<br>
<br>
> Friends,<br>
><br>
> I am a newbie to fitting molecular structures on a
volume map. I would appreciate if someone could suggest me
some guidelines to choose an optimal resolution of the map
before fitting.<br>
><br>
> Thanks,<br>
> Bala<br>
><br>
> --<br>
> C. Balasubramanian<br>
<br>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
C. Balasubramanian<br>
<br>
<br>
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<br>
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