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UCSF-Chimera/C3/Superimposing-and-Morphing/English - Revision history
2026-05-14T14:59:19Z
Revision history for this page on the wiki
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https://script.spoken-tutorial.org/index.php?title=UCSF-Chimera/C3/Superimposing-and-Morphing/English&diff=27205&oldid=prev
Snehalathak at 11:34, 1 July 2016
2016-07-01T11:34:28Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 11:34, 1 July 2016</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>press enter.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>press enter.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Next,  </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Next, to remove '''solvent '''molecules from the structure<ins class="diffchange diffchange-inline">;</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">*</del>to remove '''solvent '''molecules from the structure</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>I will select the command “'''del solvent'''”.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">*</del>I will select the command “'''del solvent'''”.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Press '''Enter'''.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Press '''Enter'''.</div></td></tr>
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Snehalathak
https://script.spoken-tutorial.org/index.php?title=UCSF-Chimera/C3/Superimposing-and-Morphing/English&diff=27199&oldid=prev
Nancyvarkey at 10:41, 1 July 2016
2016-07-01T10:41:54Z
<p></p>
<a href="https://script.spoken-tutorial.org/index.php?title=UCSF-Chimera/C3/Superimposing-and-Morphing/English&diff=27199&oldid=27115">Show changes</a>
Nancyvarkey
https://script.spoken-tutorial.org/index.php?title=UCSF-Chimera/C3/Superimposing-and-Morphing/English&diff=27115&oldid=prev
Snehalathak: Created page with " {| style="border-spacing:0;" ! <center>Visual Cue</center> ! <center>Narration</center> |- | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;..."
2016-06-22T11:45:29Z
<p>Created page with " {| style="border-spacing:0;" ! <center>Visual Cue</center> ! <center>Narration</center> |- | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;..."</p>
<p><b>New page</b></p><div><br />
{| style="border-spacing:0;"<br />
! <center>Visual Cue</center><br />
! <center>Narration</center><br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 1'''<br />
<br />
'''Title Slide'''<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Welcome to this tutorial on '''Superimposing and Morphing'''<br />
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|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 2'''<br />
<br />
'''Learning Objectives'''<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial, we will learn to<br />
<br />
<br />
'''Superimpose''' and compare different structures of the same protein.<br />
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Morph '''conformations''' and create a '''trajectory'''.<br />
<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 3'''<br />
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'''Pre-requisites'''<br />
<br />
<br />
'''spoken-tutorial.org'''<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To follow this tutorial you should be familiar with,<br />
<br />
<br />
'''Chimera''' Interface.<br />
<br />
<br />
If not, for relevant tutorials, please visit our website. <br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 4'''<br />
<br />
'''System Requirement'''<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here I am using<br />
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'''Ubuntu''' OS version. 14.04<br />
<br />
'''Chimera''' version 1.10.2<br />
<br />
'''Mozilla firefox''' browser 42.0<br />
<br />
And a working Internet connection.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Double-click on the Chimera <br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here I have opened a '''Chimera''' window.<br />
<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the file '''3w7f '''from the side panel.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| From the '''graphic access''' interface, Click on the file '''3w7f'''.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The structure of Squalin Synthase opens on the screen.<br />
<br />
<br />
Now let us prepare this structure for '''superimposing'''.<br />
<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| It contains two copies of the same protein.<br />
<br />
<br />
Using the '''command line''' delete one of the chains. <br />
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|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the small back triangle at the end of the command line.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| I will recall the command by clicking on the command history.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down the command history dialog box.<br />
<br />
<br />
Select the command “'''delete:.a'''” press enter.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| From the command history dialog box, select the command '''“delete:.a”''' <br />
<br />
<br />
press enter.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select the command “'''del solvent'''” from command history.<br />
<br />
press enter.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Next to remove '''solvent '''molecules from the structure;<br />
<br />
I will select the command “'''del solvent'''”.<br />
<br />
press enter.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This structure is bound to the substrate analog '''Farnesyl thiopyrophosphate'''. '''FPS''' in short.<br />
<br />
<br />
We will superimpose two similar proteins to compare their secondary structures.<br />
<br />
<br />
For this we will fetch a structure of the same enzyme without substrate.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| On the command line type “'''open 2zco'''” press enter.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| On the command line type “'''open 2zco'''” press enter.<br />
<br />
<br />
The new structure is in blue color.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now these two structures are ready to be superimposed.<br />
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|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 5'''<br />
<br />
'''Structural alignment'''<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Superimposition or Structural alignment''' is a tool to compare two or more protein structures.<br />
<br />
<br />
The alignment is based on their shape and three -dimensional conformation.<br />
<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Before we start superimposing, let us place some icons in the tool bar. <br />
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|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Favorites menu >>Add to favorites'''.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Favorites menu.'''<br />
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'''Scroll down to Add to favorites/Tool bar '''option.<br />
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A''' Preferences''' dialog box opens.<br />
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|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on preferences dialog box.<br />
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Under the heading “'''Settings'''”, under the “'''On Tool bar'''” column, check th boxes for:<br />
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'''Command line'''<br />
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'''Model Panel'''<br />
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'''Side View'''<br />
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'''MatchMaker '''<br />
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'''Match-Align'''<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| From the Category drop-down, select '''Tools'''.<br />
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Under the heading “'''Settings'''”, check boxes under “'''On Tool bar'''” column.<br />
<br />
<br />
Check boxes for,<br />
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'''Command line'''<br />
<br />
'''Model Panel'''<br />
<br />
'''Side View'''<br />
<br />
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Scroll down and click on,<br />
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'''MatchMaker '''<br />
<br />
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'''and Match-Align'''<br />
<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| You can customize your own tool bar.<br />
<br />
<br />
Select tools according to your requirement.<br />
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|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor pointing '''tool bar'''.<br />
<br />
<br />
Click on the '''Toolbar placement''' button.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the panel. <br />
<br />
Icons have been added to the '''Tool bar''' on top of the panel.<br />
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To change the position of the '''tool bar''', click on the '''Toolbar placement''' button.<br />
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<br />
And select the option from the drop-down menu.<br />
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|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Save''' button.<br />
<br />
Close the window.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| When you finish adding all icons to the tool bar, click on '''Save''' button.<br />
<br />
<br />
And click on '''Close''' to close the '''dialog box'''. <br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Hold the mouse button and drag on the panel. <br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The structures are now in different positions.<br />
<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.<br />
<br />
<br />
<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now let us superimpose the structures using '''MatchMaker''' function.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''MatchMaker '''tool on the''' Tool bar'''. <br />
<br />
<br />
<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''MatchMaker '''tool on the''' Tool bar'''. <br />
<br />
<br />
A '''MatchMaker''' dialog box opens. <br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on '''MatchMaker''' dialog box.<br />
<br />
<br />
Press '''OK '''button. <br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on''' 3w7f '''as Reference structure.<br />
<br />
<br />
For now let us continue with the default settings.<br />
<br />
<br />
Press '''OK''' button. <br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the panel.<br />
<br />
The two structures are '''superimposed''' on each other.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The two structures are almost completely '''superimposable''' with each other.<br />
<br />
<br />
Except for a small part which is '''non-superimposable'''.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on amino acids 53 and 57.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The fragment involved in this '''non-superimposable''' part starts from :<br />
<br />
<br />
the amino acid number 53 to amino acid number 57.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''The MatchMaker''' generates a '''sequence alignment''' using residue types and secondary structure.<br />
<br />
<br />
And then fits the '''sequence-aligned''' residues in 3D.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Match-Align''' tool.<br />
<br />
<br />
Click on the pdb Id of both the chains to select them.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let us now check the '''Match-Align''' tool.<br />
<br />
<br />
Click on''' Match-Align''' tool from the tool bar.<br />
<br />
A dialog box opens.<br />
<br />
<br />
To select the chains, click on their pdb Ids.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on OK button.<br />
<br />
<br />
Cursor on the '''sequence alignment dialog box.'''<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on OK button.<br />
<br />
A '''sequence alignment''' dialog box opens.<br />
<br />
<br />
In this box the '''amino acid '''pairs used in the final fit are shown with light orange boxes.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the '''sequence alignment dialog box.'''<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The structures are mostly similar except for the loop at residues 52-54.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Hover the cursor over one letter code.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Place the cursor over the corresponding one letter code.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the '''sequence alignment dialog box.'''<br />
<br />
<br />
Click on light orange boxes to select.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The residues from '''52 to 54''' are shifted due to the presence of gaps in the sequence.<br />
<br />
<br />
Select this part using the cursor.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Actions''' menu, Scroll down to '''Color'''. <br />
<br />
<br />
Choose any color from the sub-menu. <br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the panel.<br />
<br />
The part of the sequence selected is highlighted.<br />
<br />
<br />
This corresponds to the '''non-superimposabl'''e part of the structure.<br />
<br />
You can change the color of this '''non-superimposing''' parts using '''Actions''' menu.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Actions''' menu, scroll down to '''Color''', click on '''orange-red '''option.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Actions''' menu, scroll down to '''Color''', click on '''orange-red '''option.<br />
<br />
<br />
Now this part is highlighted.<br />
<br />
<br />
Clear the selection and close the dialog box.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now let me demonstrate how to morph '''conformations''' and create a trajectory.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 6'''<br />
<br />
'''Morphing'''<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Morphing involves calculating a series of intermediate structures between the original input structures.<br />
<br />
<br />
The series of intermediate structures created can be saved as '''Molecular Dynamics Movie '''in short''' MD Movie.'''<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Tools menu >> Structure Comparison >> Morph conformations.''' <br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Back to the panel.<br />
<br />
Start the morphing tool from the '''Tools''' menu.<br />
<br />
Click on '''Tools menu scroll down to Structure Comparison.'''<br />
<br />
'''Click on Morph conformations '''option'''.'''<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the Morph conformations dialog box.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A '''Morph conformations''' dialog box opens.<br />
<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Add '''button.<br />
<br />
<br />
In Model dialog, double click on model number 0 and model number 1.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Add.'''<br />
<br />
<br />
In the resulting list of the models dialog box;<br />
<br />
<br />
double click on model number zero, that is '''3w7f''' to add to the conformations.<br />
<br />
<br />
Next click on model number 1 that is '''2zco'''.<br />
<br />
Then again click on '''3w7f''', that is model number zero.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the Morph conformations dialog box.<br />
<br />
<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This sequence corresponds to a morph '''trajectory''':<br />
<br />
<br />
From ligand bound to the structure to empty structure and then back.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on x button.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Close the '''model list''' dialog.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Create''' in the Morph conformations dialog.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Create''' in the Morph conformations dialog box.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the dialog box.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| After a few seconds a''' MD Movie''' is created. <br />
<br />
<br />
The dialog box appears on the screen. <br />
<br />
<br />
The dialog box has buttons to play or pause the movie.<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on arrow button.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on the arrow button to play.<br />
<br />
<br />
Observe the panel. <br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The morphing of conformations is being played as a movie.<br />
<br />
Pause the movie and close the MD movie dialog box.<br />
<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 7'''<br />
<br />
Summary<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now Lets summarize what we have learnt.<br />
<br />
<br />
In this tutorial we have learnt to,<br />
<br />
<br />
'''Superimpose '''and compare different structures of the same protein.<br />
<br />
<br />
Morph '''conformations''' and create a '''trajectory'''.<br />
<br />
<br />
Save the trajectory as '''Molecular Dynamics Movie.'''<br />
<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 8'''<br />
<br />
Assignment<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For the assignment,<br />
<br />
<br />
Open the structures of '''GTP binding '''proteins with the '''PDB code''': '''1TAG''' and '''1TND'''<br />
<br />
<br />
Superimpose the structures using '''MatchMaker''' tool. <br />
<br />
<br />
Using '''Sequence Alignment''' tool, find out the regions that are non-identical. <br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 9'''<br />
<br />
'''Acknowledgement '''<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The video at the following link summarizes the '''Spoken Tutorial project. '''<br />
<br />
Please download and watch it. <br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 10'''<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The '''Spoken Tutorial Project''' Team conducts workshops and gives certificates for those who pass an online test. <br />
<br />
For more details, please write to us. <br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 11'''<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Spoken Tutorial Project''' is funded by '''NMEICT, MHRD, Government of India. '''<br />
<br />
More information on this '''Mission''' is available at the link shown<br />
<br />
|-<br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| <br />
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This is '''Snehalatha''' from '''IIT Bombay''' signing off. Thank you for joining. <br />
<br />
|}</div>
Snehalathak