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	<title>My software notes</title>
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	<link>http://kpwu.wordpress.com</link>
	<description>a site collecting reports/tests/notes of software/programs related to NMR, linux,and Mac</description>
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		<title>My software notes</title>
		<link>http://kpwu.wordpress.com</link>
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			<item>
		<title>[QuteMol] another molecular viewer</title>
		<link>http://kpwu.wordpress.com/2009/04/01/qutemol/</link>
		<comments>http://kpwu.wordpress.com/2009/04/01/qutemol/#comments</comments>
		<pubDate>Thu, 02 Apr 2009 04:16:57 +0000</pubDate>
		<dc:creator>kpwu</dc:creator>
				<category><![CDATA[pymol/ molmol]]></category>
		<category><![CDATA[QuteMol]]></category>

		<guid isPermaLink="false">http://kpwu.wordpress.com/?p=210</guid>
		<description><![CDATA[I learned a new molecular viewer called QuteMol. Like the name, it displays the molecules in a cute way. I like the way QuteMol simulates SEM-like structure. It&#8217;s good for a manual assembeled supramolecules (e.g. GroEL+GroES); you can display the PDB structure in a SEM-like picture.
So far, QuteMol supports platform includes MS-Win and Mac OS.
Here [...]<img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=210&subd=kpwu&ref=&feed=1" />]]></description>
			<content:encoded><![CDATA[<div class='snap_preview'><br /><p>I learned a new molecular viewer called <a href="http://qutemol.sourceforge.net/" target="_blank">QuteMol</a>. Like the name, it displays the molecules in a cute way. I like the way QuteMol simulates SEM-like structure. It&#8217;s good for a manual assembeled supramolecules (e.g. GroEL+GroES); you can display the PDB structure in a SEM-like picture.</p>
<p>So far, QuteMol supports platform includes MS-Win and Mac OS.</p>
<p>Here is my example using 1XQ8:</p>
<p><img class="alignnone size-full wp-image-214" title="1xq8pdb1" src="http://kpwu.files.wordpress.com/2009/04/1xq8pdb1.png?w=400&#038;h=400" alt="1xq8pdb1" width="400" height="400" /></p>
<p>Or 2C7D, a GroEL+GroES complex.<br />
<img src="http://kpwu.files.wordpress.com/2009/04/2c7dpdb1.png?w=512&#038;h=512" alt="2c7dpdb1" title="2c7dpdb1" width="512" height="512" class="alignnone size-full wp-image-219" /></p>
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			<media:title type="html">1xq8pdb1</media:title>
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		<item>
		<title>[PyMOL] give your protein a box!</title>
		<link>http://kpwu.wordpress.com/2009/03/27/pymol-give-your-protein-a-box/</link>
		<comments>http://kpwu.wordpress.com/2009/03/27/pymol-give-your-protein-a-box/#comments</comments>
		<pubDate>Sat, 28 Mar 2009 05:35:08 +0000</pubDate>
		<dc:creator>kpwu</dc:creator>
				<category><![CDATA[pymol/ molmol]]></category>

		<guid isPermaLink="false">http://kpwu.wordpress.com/?p=200</guid>
		<description><![CDATA[Here is a nice script to draw a minimu bounding box of your target PDB.
Author: Jason Vertrees
Example of 2GB1, using stereo view:

usage:
run PATH/drawMinBoundingBox.py
drawMinBoundingBox.py 2GB1, 3, r=0.3, g=0.3, b=0.3
======
drawMinBoundingBox [selection, [lineWidth, [redColor, [greenColor, [blueColor]]]]]
Download this script at pymolwiki.
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			<content:encoded><![CDATA[<div class='snap_preview'><br /><p>Here is a <a href="http://www.pymolwiki.org/index.php/DrawMinBoundingBox" target="_blank">nice script</a> to draw a minimu bounding box of your target PDB.<br />
Author: Jason Vertrees</p>
<p>Example of 2GB1, using stereo view:<br />
<a href="http://kpwu.files.wordpress.com/2009/03/2gb1-box.png?"><img class="alignnone size-medium wp-image-202" title="2gb1-box" src="http://kpwu.files.wordpress.com/2009/03/2gb1-box.png?w=300&#038;h=189" alt="2gb1-box" width="300" height="189" /></a></p>
<p>usage:<br />
run PATH/drawMinBoundingBox.py<br />
drawMinBoundingBox.py 2GB1, 3, r=0.3, g=0.3, b=0.3<br />
======<br />
drawMinBoundingBox [selection, [lineWidth, [redColor, [greenColor, [blueColor]]]]]</p>
<p><a href="http://www.pymolwiki.org/images/7/78/DrawMinBoundBox.tar.bz2" target="_blank">Download this script at pymolwiki.</a></p>
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			<media:title type="html">2gb1-box</media:title>
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	</item>
		<item>
		<title>[IDP] Cytoplasmic Domain of the T Cell Receptor zeta</title>
		<link>http://kpwu.wordpress.com/2008/12/10/idp-cytoplasmic-domain-of-the-t-cell-receptor-zeta/</link>
		<comments>http://kpwu.wordpress.com/2008/12/10/idp-cytoplasmic-domain-of-the-t-cell-receptor-zeta/#comments</comments>
		<pubDate>Thu, 11 Dec 2008 02:31:44 +0000</pubDate>
		<dc:creator>kpwu</dc:creator>
				<category><![CDATA[IDP]]></category>

		<guid isPermaLink="false">http://kpwu.wordpress.com/?p=197</guid>
		<description><![CDATA[Title:  The Intrinsically Disordered Cytoplasmic Domain of the T Cell Receptor ζ Chain Binds to the Nef Protein of Simian Immunodeficiency Virus without a Disorder-to-Order Transition
Authors: Alexander B. Sigalov, Walter M. Kim, Maria Saline and Lawrence J. Stern
Journal: Biochemistry, 2008, 47 (49), pp 12942–12944
Not fully labeled in HSQC

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			<content:encoded><![CDATA[<div class='snap_preview'><br /><p>Title:  The Intrinsically Disordered Cytoplasmic Domain of the T Cell Receptor ζ Chain Binds to the Nef Protein of Simian Immunodeficiency Virus without a Disorder-to-Order Transition</p>
<p>Authors: Alexander B. Sigalov, Walter M. Kim, Maria Saline and Lawrence J. Stern</p>
<p>Journal: <a href="http://pubs.acs.org/doi/full/10.1021/bi801602p">Biochemistry, 2008, 47 (49), pp 12942–12944</a></p>
<p>Not fully labeled in HSQC</p>
<p><img class="alignnone size-medium wp-image-198" title="bi-2008-01602p_0002" src="http://kpwu.files.wordpress.com/2008/12/bi-2008-01602p_0002.gif?w=129&#038;h=300" alt="bi-2008-01602p_0002" width="129" height="300" /></p>
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		<title>[IDP] RTX calcium-binding motifs</title>
		<link>http://kpwu.wordpress.com/2008/12/10/idp-rtx-calcium-binding-motifs/</link>
		<comments>http://kpwu.wordpress.com/2008/12/10/idp-rtx-calcium-binding-motifs/#comments</comments>
		<pubDate>Thu, 11 Dec 2008 02:22:41 +0000</pubDate>
		<dc:creator>kpwu</dc:creator>
				<category><![CDATA[IDP]]></category>

		<guid isPermaLink="false">http://kpwu.wordpress.com/?p=194</guid>
		<description><![CDATA[Title:RTX calcium-binding motifs are intrinsically disordered in the absence of calcium: Implication for protein secretion
Authors:    Alexandre Chenal, J. Iñaki Guijarro, Bertrand Raynal, Muriel Delepierre,  and Daniel Ladant 
Journal: J. Biol. Chem, 10.1074/jbc.M807312200 (online publish first)
Note: Not an NMR-based study.

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			<content:encoded><![CDATA[<div class='snap_preview'><br /><p>Title:RTX calcium-binding motifs are intrinsically disordered in the absence of calcium: Implication for protein secretion</p>
<p>Authors:   <strong> Alexandre Chenal, J. Iñaki Guijarro, Bertrand Raynal, Muriel Delepierre,  and Daniel Ladant </strong></p>
<p>Journal: <span><a href="http://www.jbc.org/cgi/content/abstract/M807312200v1">J. Biol. Chem, 10.1074/jbc.M807312200</a> (online publish first)</span></p>
<p><span>Note: Not an NMR-based study.<br />
</span></p>
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		<title>[IDP] Human Securin</title>
		<link>http://kpwu.wordpress.com/2008/12/10/idp-human-securin/</link>
		<comments>http://kpwu.wordpress.com/2008/12/10/idp-human-securin/#comments</comments>
		<pubDate>Wed, 10 Dec 2008 17:58:35 +0000</pubDate>
		<dc:creator>kpwu</dc:creator>
				<category><![CDATA[IDP]]></category>
		<category><![CDATA[NMR]]></category>

		<guid isPermaLink="false">http://kpwu.wordpress.com/?p=190</guid>
		<description><![CDATA[Title:Structural and Dynamic Characterization of Intrinsically Disordered Human Securin by NMR Spectroscopy
Authors: Veronika Csizmok, Isabella C. Felli, Peter Tompa, Lucia Banci and Ivano Bertin
Journal: J. Am. Chem. Soc., 2008, 130 (50), pp 16873–16879
Assignment table is provided within the supplementary file.

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			<content:encoded><![CDATA[<div class='snap_preview'><br /><p>Title:Structural and Dynamic Characterization of Intrinsically Disordered Human Securin by NMR Spectroscopy</p>
<p>Authors: Veronika Csizmok, Isabella C. Felli, Peter Tompa, Lucia Banci and Ivano Bertin</p>
<p>Journal: <a href="http://pubs.acs.org/doi/full/10.1021/ja805510b">J. Am. Chem. Soc., 2008, 130 (50), pp 16873–16879</a></p>
<p>Assignment table is provided within the supplementary file.</p>
<p><img class="alignnone size-medium wp-image-191" title="ja-2008-05510b_0002" src="http://kpwu.files.wordpress.com/2008/12/ja-2008-05510b_0002.gif?w=300&#038;h=206" alt="ja-2008-05510b_0002" width="300" height="206" /></p>
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