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<div class="moz-cite-prefix">Hi Rakesh,<br>
<br>
The Chimera web proxy settings in Preferences / Web Access do
not support proxy servers which require authentication. Chimera
is using the Python language urllib module http_proxy environment
variable described here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://docs.python.org/library/urllib.html">http://docs.python.org/library/urllib.html</a><br>
<br>
and it says if this variable is not used then the proxy settings
are obtained on Windows from the registry's Internet Settings
section. You also might be able to set the http_proxy environment
variable yourself including the user name and password as
described at the bottom (Oct 15, 2010) of this discussion<br>
<br>
<a class="moz-txt-link-freetext" href="http://stackoverflow.com/questions/34079/how-to-specify-an-authenticated-proxy-for-a-python-http-connection">http://stackoverflow.com/questions/34079/how-to-specify-an-authenticated-proxy-for-a-python-http-connection</a><br>
<br>
I've made a Chimera bug database entry for this problem but think
you will need to solve this outside of Chimera.<br>
<br>
<a class="moz-txt-link-freetext" href="http://plato.cgl.ucsf.edu/trac/chimera/ticket/11212">http://plato.cgl.ucsf.edu/trac/chimera/ticket/11212</a><br>
<br>
You can google for Giovanni and get his email. It was in the
top hit searching for Giovanni Cardone NIH.<br>
<br>
Supplementary figure 5 of "
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GTPase activation of elongation factor EF-Tu by the ribosome
during decoding", Schuette, et al. says "The local CCC was
calculated within a moving box (size 9x9x9 pixels at 1.26 Å pixel
size) in steps of 4 pixels.
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<link rel="File-List"
href="file://localhost/Users/goddard/Library/Caches/TemporaryItems/msoclip/0clip_filelist.xml">
<link rel="themeData"
href="file://localhost/Users/goddard/Library/Caches/TemporaryItems/msoclip/0clip_themedata.xml">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Arial;
panose-1:2 11 6 4 2 2 2 2 2 4;
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</style>" Although the figure caption says it was made with Chimera,
that moving box calculation is not a Chimera capability and they
must have written their own code or used someone else's code to do
that and you would need to ask them.<br>
<br>
Tom<br>
<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] Doubt regarding cryeom map density
threshold setting<br>
From: rakesh ramachandram <br>
To: Tom Goddard <br>
Date: 7/24/12 11:26 AM<br>
<blockquote type="cite">Hi,<br>
<br>
Thanks for the message. I tried the webservice without proxy
but unable to connect it. I was trying to fetch the pdb and for
homology modeling. Moreover the report a bug option is also not
working since it is unable to connect to internet.<br>
<br>
Do you have the email id of Giovanni Cardone so that I can
write to him for the plugin. I recently saw its use in two
papers.<br>
<br>
I saw a method in this article "<font>GTPase activation of
elongation factor EF-Tu by the ribosome during decoding</font>"
in EMBO journal where for generating supplementary figure 5 they
have used chimera and colored according to the cross correlation
value with a threshold. I would be grateful if you can explain
me the methodology after you read it and how to generate it in
chimera.<br>
<br>
Regards<br>
Rakesh<br>
<br>
<div class="gmail_quote">On 24 July 2012 22:51, Tom Goddard <span
dir="ltr"></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>
<div class="im">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>
</div>
<a
href="http://www.cgl.ucsf.edu/chimera/docs/webservices.html"
target="_blank">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.<span
class="HOEnZb"><font color="#888888"><br>
<br>
Tom<br>
<br>
<br>
<br>
</font></span></div>
<div>
<div class="h5">
<blockquote 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"></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
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><font
color="#888888"><br>
<br>
Tom<br>
<br>
</font></span></div>
<div>
<div>
<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>
</div>
</blockquote>
</div>
<br>
</blockquote>
<br>
<br>
</div>
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</blockquote>
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<br>
</blockquote>
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