User:Wayne Decatur/Sandbox: Difference between revisions

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<scene name='User:Wayne_Decatur/Sandbox/Test/3'>TextToBeDisplayed</scene>
<scene name='User:Wayne_Decatur/Sandbox/Test/3'>TextToBeDisplayed</scene>


[[Help:Protected_Pages|'''here''']] link with 3 quotes<br>
[[Help:Protected_Pages|''here'']] link with 2 quotes<br>
[[Help:Protected_Pages|here]] link with  no quotes<br>


==HOW TO MAKE AN ANIMATION USING PROTEOPEDIA SCREEN AUTHORING TOOLS AND THE CONSOLE==
==HOW TO MAKE AN ANIMATION USING PROTEOPEDIA SCREEN AUTHORING TOOLS AND THE CONSOLE==


<applet load='2hty2hu4_j.pdb' size='500' frame='true' align='right' caption='Morph of N1 alone (2hty) to N1 complexed with Tamiflu (2hu4). The position where Tamiflu will bind is shown translucent except when bound in the empirically-determined model.' scene='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/2' />
<applet load='2hty2hu4_j.pdb' size='500' frame='true' align='right' caption='Morph of N1 alone (2hty) to N1 complexed with Tamiflu (2hu4). The position where Tamiflu will bind is shown translucent except when bound in the empirically-determined model.' scene='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/2' />
Tamiflu was designed to fit N2/N9, so it is serendipitous that it works on N1. In fact, when the structure of N1 was determined<ref name='Russell2006' />, the <font color='#e07000'><b>loop comprising residues 147-152</b></font> was not in a suitable position to participate in binding Tamiflu. However, the complex of N1 with Tamiflu revealed that this loop is pulled into proper contact with the drug in an [[Induced fit|induced fit]] manner<ref name='Russell2006' />. A [[Morphs|morph]] from N1 alone ([[2hty]]) to N1 complexed with Tamiflu ([[2hu4]])<ref>Chain A from [[2hty]] was morphed to chain A of [[2hu4]] by linear interpolation, inserting 6 intermediate interpolated frames, using the freely available [http://www.umass.edu/microbio/rasmol/pdbtools.htm#martz morph2 program].</ref> shows the change in position of this loop (<scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/8'>replay initial morph</scene>).
T
s, <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/7'>Asp151, Glu119</scene>, closer to the inhibitor.
 
 
 
Here is the<br>
<scene name='User:Wayne_Decatur/Sandbox/Test_animation/1'>test animation WAYNE made here on this page</scene>
<!--HOW TO MAKE AN ANIMATION USING PROTEOPEDIA SCREEN AUTHORING TOOLS AND THE CONSOLE
model 0;select all; spacefill on;
that set up default display and then I loaded 2hty2hu4_j.pdb using load molecule under Scene authoring tools
then in console, entered 'select 1.8' to select 8th model in file and then described how to display that particular model of the file that has 8 models:
select 1.8; spacefill 0.2;wireframe 0.1; color red;
anim mode palindrome;
anim on;
anim fps 8; # frames per second -->
 
 
<scene name='User:Wayne_Decatur/Sandbox/Test_animation/3'>all in scene authoring tools with checked box</scene>
 
 
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WEIRD thing with configuration I saw on October 24th 2009. When I enter 'configuration 1;' or 'configuration 2;' console in Proteopedia SAT, then it added weird lines from bases and among protein that were faint but I couldn't get rid of. It wouldn't happen in the newest version of FirstGlance linked to 1rpu page but then later it even wouldn't happen in SAT when I initiated new browser windows and JAVA runs. At first I thought it was leaving off the semi-colon but then it seemed to work with the semi-colon everywhere too. So another weird thing like when you need to scroll side of browser window to get a stuck animation going.
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==HOW TO on REFS==
This is a sample <ref>Richardson DC, Richardson JS. The kinemage: a tool for scientific communication.
Protein Sci. 1992 1:3-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1304880 1304880]</ref> of the
standard references and one <ref>PMID:18673581</ref> with the PubmedID only new option <nowiki>"<ref>PMID:18673581</ref>"</nowiki>.


The binding of Tamiflu to N1 pulls the sidechains of two conserved residues, <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/7'>Asp151, Glu119</scene>, closer to the inhibitor.
It's possible now to have additional references by adding them to the group '''xtra'''.
See this page source under ''Additional Literature and Resources''.


== References ==
<references/>


<scene name='User:Wayne_Decatur/Sandbox/Test_animation/1'>TextToBeDisplayed</scene>
== Additional Literature and Resources ==
<ref group="xtra">PMID:15068885</ref><ref group="xtra">PMID:14749769</ref><ref group="xtra">PMID:1304880</ref><ref group="xtra">PMID:16270100</ref><ref group="xtra">PMID:14661029</ref> <!--Putting all on one line eliminates blank space at top-->
<references group="xtra"/>
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