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<div class="moz-cite-prefix">Hi Rakesh,<br>
<br>
Chimera is not able to compute the local resolution of an EM
map. Giovanni Cardone at the NIH has made a Chimera plug-in that
does this and he talked about it at the 2011 3DEM Gordon
conference. I don't know whether he ever distributed it. You
should ask him.<br>
<br>
Also Chimera does not have any method for computing local
cross-correlation between a PDB model and a map. That would be
nice. Is there a journal article evaluating a specific method for
doing that?<br>
<br>
For your Chimera internet connection problem it would help to
know what Chimera web service you are trying to use. Are you
fetching a PDB model? building a homology model? running BLAST?
getting Uniprot annotations? Chimera has lots of web services<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.cgl.ucsf.edu/chimera/docs/webservices.html">http://www.cgl.ucsf.edu/chimera/docs/webservices.html</a><br>
<br>
and perhaps some do not use the proxy setting in Chimera /
Preferences / Web Access. You could use Chimera menu Help /
Report a Bug... to get help on this problem -- probably better
than using the mailing list.<br>
<br>
Tom<br>
<br>
<br>
<br>
</div>
<blockquote
cite="mid:CAEYPXnbK6T7naghmrM+h6O=Lgwx50rvk-wqTO6LcjMr=w3iYBA@mail.gmail.com"
type="cite">Hi,<br>
<br>
I want to know how to color the cryoem map according to the
local resolution and also according to the local cross correlation
of the pdb structure with the map.<br>
<br>
Moreover I am unable to connect to the internet in chimera
inspite of providing the proxy address and port, how should I give
the user name and password for authentication to connect inside
chimera since I get authentication error.<br>
<br>
Regards<br>
Rakesh<br>
<br>
<div class="gmail_quote">On 7 July 2012 03:48, Tom Goddard <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:goddard@sonic.net" target="_blank">goddard@sonic.net</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>You can choose a map contour so it encloses the
expected number of cubic Angstroms as described here:<br>
<br>
<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/data/tutorials/eman07/chimera-eman-2007.html#part2"
target="_blank">http://www.cgl.ucsf.edu/chimera/data/tutorials/eman07/chimera-eman-2007.html#part2</a><span
class="HOEnZb"><font color="#888888"><br>
<br>
Tom<br>
<br>
</font></span></div>
<div>
<div class="h5">
<blockquote type="cite">Hello,<br>
<br>
My name is Rakesh. I would like to know how to
set the density threshold according to the molecular
mass of the protein in the cryoem map. I would also
like to know how to calculate the molecular mass of a
particular segment after segmentation in cryoem map.<br>
<br>
<pre style="font-family:arial,helvetica,sans-serif"><font>Regards
Rakesh Ramachandran
PhD Student
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore - 560012
India</font>
</pre>
</blockquote>
<br>
</div>
</div>
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</blockquote>
</div>
<br>
</blockquote>
<br>
<br>
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