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		<id>https://script.spoken-tutorial.org/index.php?title=UCSF-Chimera/C2/Writing-Commands/English&amp;diff=25895&amp;oldid=prev</id>
		<title>Nancyvarkey at 09:32, 24 February 2016</title>
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				<updated>2016-02-24T09:32:02Z</updated>
		
		<summary type="html">&lt;p&gt;&lt;/p&gt;
&lt;a href=&quot;https://script.spoken-tutorial.org/index.php?title=UCSF-Chimera/C2/Writing-Commands/English&amp;amp;diff=25895&amp;amp;oldid=25858&quot;&gt;Show changes&lt;/a&gt;</summary>
		<author><name>Nancyvarkey</name></author>	</entry>

	<entry>
		<id>https://script.spoken-tutorial.org/index.php?title=UCSF-Chimera/C2/Writing-Commands/English&amp;diff=25858&amp;oldid=prev</id>
		<title>Snehalathak: Created page with &quot;{| style=&quot;border-spacing:0;&quot; ! &lt;center&gt;Visual Cue&lt;/center&gt; ! &lt;center&gt;Narration&lt;/center&gt;  |- | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;b...&quot;</title>
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				<updated>2016-02-23T11:25:29Z</updated>
		
		<summary type="html">&lt;p&gt;Created page with &amp;quot;{| style=&amp;quot;border-spacing:0;&amp;quot; ! &amp;lt;center&amp;gt;Visual Cue&amp;lt;/center&amp;gt; ! &amp;lt;center&amp;gt;Narration&amp;lt;/center&amp;gt;  |- | style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;b...&amp;quot;&lt;/p&gt;
&lt;p&gt;&lt;b&gt;New page&lt;/b&gt;&lt;/p&gt;&lt;div&gt;{| style=&amp;quot;border-spacing:0;&amp;quot;&lt;br /&gt;
! &amp;lt;center&amp;gt;Visual Cue&amp;lt;/center&amp;gt;&lt;br /&gt;
! &amp;lt;center&amp;gt;Narration&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| '''Slide Number 1'''&lt;br /&gt;
&lt;br /&gt;
'''Title Slide'''&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| Welcome to this tutorial on '''Writing Commands '''in '''Chimera'''.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| '''Slide Number 2'''&lt;br /&gt;
&lt;br /&gt;
'''Learning Objectives'''&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| In this tutorial, we will type commands to,&lt;br /&gt;
&lt;br /&gt;
* Change the '''display''' to atoms.&lt;br /&gt;
* Show and hide '''ribbons'''.&lt;br /&gt;
* Change the color of the '''amino acid residues.'''&lt;br /&gt;
* Label individual '''residues'''.&amp;lt;br/&amp;gt; &lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| '''Slide Number 3'''&lt;br /&gt;
&lt;br /&gt;
'''Learning Objectives'''&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;|&lt;br /&gt;
&lt;br /&gt;
* Remove '''solvent''' molecules. &lt;br /&gt;
* And save the image in different file formats.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| '''Slide Number 4'''&lt;br /&gt;
&lt;br /&gt;
'''Pre-requisites'''&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| To follow this tutorial you should have knowledge of,&lt;br /&gt;
&lt;br /&gt;
Undergraduate '''Biochemistry'''&lt;br /&gt;
&lt;br /&gt;
Must be familiar with, '''Structural Biology '''&lt;br /&gt;
&lt;br /&gt;
and '''Chimera interface'''. &lt;br /&gt;
&lt;br /&gt;
For relevant tutorials, please visit our website. &lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| '''Slide Number 5'''&lt;br /&gt;
&lt;br /&gt;
'''System Requirement'''&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| To record this tutorial, I am using&lt;br /&gt;
&lt;br /&gt;
'''Ubuntu OS version'''. 14.04&lt;br /&gt;
&lt;br /&gt;
'''Chimera''' '''version''' 1.10.2&lt;br /&gt;
&lt;br /&gt;
'''Mozilla firefox browser''' 42.0&lt;br /&gt;
&lt;br /&gt;
And a working '''Internet connection'''.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Click on the Chimera icon. &lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| Double-click on the '''Chimera''' icon to open the '''Chimera''' window.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Click on the lightning bolt icon.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| Click on the '''lightning bolt icon''' to open the '''graphics window'''.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Cursor on the panel.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Click on''' Favorites''' menu, scroll down.&lt;br /&gt;
&lt;br /&gt;
Click on C'''ommand line '''option. &lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| In this tutorial,&lt;br /&gt;
&lt;br /&gt;
I will demonstrate how to use '''commands''' to manipulate the structure. &lt;br /&gt;
&lt;br /&gt;
Open the '''Command Line''' using '''Favorites''' menu.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Point to the command &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Cursor on the '''Command line'''.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| A '''command text box''' appears at the bottom of the C'''himera''' window.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Tasks, performed with '''menus '''can be carried out using '''commands'''.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| '''Slide Number 6'''&lt;br /&gt;
&lt;br /&gt;
'''Chimera Commands'''&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| About '''Chimera Commands'''.&lt;br /&gt;
&lt;br /&gt;
'''Chimera commands''' are entered at the''' Command line.'''&lt;br /&gt;
&lt;br /&gt;
Multiple '''commands '''can be combined into one line with '''semicolon''' separators.&lt;br /&gt;
&lt;br /&gt;
Press '''Enter key''' to execute the '''command'''.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| '''Slide number 7'''&lt;br /&gt;
&lt;br /&gt;
'''Chimera Commands'''&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| Previous '''commands''' can be accessed from '''command History.'''&lt;br /&gt;
&lt;br /&gt;
More information about '''commands''' is given at the link shown. &lt;br /&gt;
&lt;br /&gt;
'''http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecore.html'''&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Cursor on the command line.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| Back to the '''Chimera''' '''window'''.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Let us open a model of '''leucine zipper''' by typing a '''command'''.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| On the command line text box type '''open 1zik'''.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| The '''command''' starts with a '''command''' word.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
On the command line text box type, &lt;br /&gt;
&lt;br /&gt;
'''open space 1zik'''.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
You need a working '''Internet connection''' for this step.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Press enter.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| Press''' enter''' to execute the '''command'''.&lt;br /&gt;
&lt;br /&gt;
The structure appears on the screen.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Type:&lt;br /&gt;
&lt;br /&gt;
'''display '''&lt;br /&gt;
&lt;br /&gt;
Press enter.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| To change the '''ribbons''' display to atoms, &lt;br /&gt;
&lt;br /&gt;
In the '''command line text box''' type:&lt;br /&gt;
&lt;br /&gt;
The''' Command '''word''' display '''&lt;br /&gt;
&lt;br /&gt;
Press '''enter'''. &lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Cursor on the panel.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| We now have the structure of the protein in atoms display. &lt;br /&gt;
&lt;br /&gt;
The structure is partially represented as '''ribbons'''.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Type:&lt;br /&gt;
&lt;br /&gt;
'''~ ribbon''' &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Press enter.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| To hide the '''ribbons''',&lt;br /&gt;
&lt;br /&gt;
Type, the wave symbol, also known as '''tilda '''followed by the command word '''ribbon.'''&lt;br /&gt;
&lt;br /&gt;
A '''command''' with a '''tilda''' indicates the reverse function.&lt;br /&gt;
&lt;br /&gt;
Here, '''tilda''' symbol followed by''' ribbon keyword''' hides the '''ribbons'''.&lt;br /&gt;
&lt;br /&gt;
press enter.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Cursor on the panel.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| We can use color '''command''' to set colors to atoms, bonds, surfaces etc. &lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Type:&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''color yellow :leu'''&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| For example to change the color of all '''leucines''' &lt;br /&gt;
&lt;br /&gt;
Type:&lt;br /&gt;
&lt;br /&gt;
'''Color space yellow space colon''' :&lt;br /&gt;
&lt;br /&gt;
followed by the three letter abreviation for the amino acid.&lt;br /&gt;
&lt;br /&gt;
For '''leucine''', I will type '''leu '''&lt;br /&gt;
&lt;br /&gt;
Here '''color''' is '''command word''' with argument as yellow and target is all''' leucines''' in the structure.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Cursor on the command line.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| If you do not specify a target the entire structure will be colored in yellow.&lt;br /&gt;
&lt;br /&gt;
Press '''enter '''&lt;br /&gt;
&lt;br /&gt;
Observe the '''panel'''. All the '''leucines''' are now colored yellow&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Cursor on the command line.&lt;br /&gt;
&lt;br /&gt;
Type &lt;br /&gt;
&lt;br /&gt;
'''color red :18.A '''&lt;br /&gt;
&lt;br /&gt;
Press enter &lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| We can specifically color an '''amino acid''' present at a particular location.&lt;br /&gt;
&lt;br /&gt;
For example to change the color of''' histidine''' present at position 18 on '''chain B''': &lt;br /&gt;
&lt;br /&gt;
Type &lt;br /&gt;
&lt;br /&gt;
'''color space red space colon18.B'''&lt;br /&gt;
&lt;br /&gt;
Press enter &lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Cursor on the panel.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| Observe the panel, '''histidine''' is now colored in''' red'''.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Type&lt;br /&gt;
&lt;br /&gt;
'''rep sphere'''&lt;br /&gt;
&lt;br /&gt;
Press enter&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| To change the display of the entire structure to '''CPK '''spacefill, &lt;br /&gt;
&lt;br /&gt;
Type,&lt;br /&gt;
&lt;br /&gt;
'''rep '''(rep is the truncated version for the keyword '''represent''' ) &lt;br /&gt;
&lt;br /&gt;
rep '''space sphere'''&lt;br /&gt;
&lt;br /&gt;
Press '''enter'''.&lt;br /&gt;
&lt;br /&gt;
Observe the panel.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Type,&lt;br /&gt;
&lt;br /&gt;
'''rep stick'''&lt;br /&gt;
&lt;br /&gt;
press enter.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| To bring back the structure to '''stick''' display.&lt;br /&gt;
&lt;br /&gt;
Again type,&lt;br /&gt;
&lt;br /&gt;
'''rep space stick'''&lt;br /&gt;
&lt;br /&gt;
Press''' enter'''&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Type&lt;br /&gt;
&lt;br /&gt;
'''del solvent'''&lt;br /&gt;
&lt;br /&gt;
Press enter &lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| To hide the''' solvent''' molecules from the structure,&lt;br /&gt;
&lt;br /&gt;
Type&lt;br /&gt;
&lt;br /&gt;
'''del for delete space solvent'''&lt;br /&gt;
&lt;br /&gt;
Press enter. &lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Type,&lt;br /&gt;
&lt;br /&gt;
'''Select :18.A '''&lt;br /&gt;
&lt;br /&gt;
Press enter&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Type,&lt;br /&gt;
&lt;br /&gt;
'''select :28.B '''&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| To activate '''residues''' for selection, use '''select''' '''command''' word.&lt;br /&gt;
&lt;br /&gt;
On the '''command line''' text box type,&lt;br /&gt;
&lt;br /&gt;
'''Select space colon '''followed by the number and '''chain''' of the residue.&lt;br /&gt;
&lt;br /&gt;
For example to activate the '''lysine''' present at the position 28, on''' chain B''' &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Type,&lt;br /&gt;
&lt;br /&gt;
'''select space colon '''followed by''' 28 dot B '''&lt;br /&gt;
&lt;br /&gt;
Press enter&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Type&lt;br /&gt;
&lt;br /&gt;
'''rlabel sel'''&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Press enter&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| Now to show the '''label''' for the '''residue''' selected,&lt;br /&gt;
&lt;br /&gt;
Type&lt;br /&gt;
&lt;br /&gt;
'''rlabel space sel'''&lt;br /&gt;
&lt;br /&gt;
Press enter&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Cursor on the panel.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| Observe the panel the '''residue label''' for the selected '''residue''' is displayed.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| press up arrow key to get the select command('''select :28.B) '''&lt;br /&gt;
&lt;br /&gt;
Type,&lt;br /&gt;
&lt;br /&gt;
'''~select :28.B '''&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| To deselect the '''residue''' which we have selected earlier:&lt;br /&gt;
&lt;br /&gt;
Press up arrow key to get the select '''command'''.&lt;br /&gt;
&lt;br /&gt;
Type the '''tilda''' symbol at the beginning of the '''command'''.&lt;br /&gt;
&lt;br /&gt;
Press enter. &lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Scroll down the commands index page.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| A list of keywords and '''command index''' is available in the '''Help menu'''.&lt;br /&gt;
&lt;br /&gt;
Click on the '''Help''' '''menu''', scroll down and click on '''Commands index'''.&lt;br /&gt;
&lt;br /&gt;
A '''web-page '''opens with the list of '''keywords''' to write '''commands'''. &lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Type:&lt;br /&gt;
&lt;br /&gt;
'''background solid blue'''&lt;br /&gt;
&lt;br /&gt;
Press enter. &lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| Back to the '''Chimera''' window.&lt;br /&gt;
&lt;br /&gt;
If you want to change the background color from black to blue.&lt;br /&gt;
&lt;br /&gt;
Type:&lt;br /&gt;
&lt;br /&gt;
'''background space solid space blue'''&lt;br /&gt;
&lt;br /&gt;
Press enter. &lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Cursor on the panel.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| The panel is now in blue color.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Click on the black triangle present at the right side of the '''Command line'''.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| To view the '''Command''' History:&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Click on the black triangle present at the right side of the '''Command line'''.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Cursor on the Command history.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Click on any command.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| The '''Command History''' lists previously used '''commands.'''&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
'''Commands''' can be re-executed by clicking on the '''command'''.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Click on '''Hide command line''' option.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| To hide the command line click on '''Hide command line''' option in the drop down.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Click on '''File''' menu. Scroll down.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| There are many options to '''save '''the structure you have created.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Open the '''File menu.'''&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Scroll down the '''File''' menu.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| You can:&lt;br /&gt;
&lt;br /&gt;
'''Restore a Session'''&lt;br /&gt;
&lt;br /&gt;
'''Save a Session'''&lt;br /&gt;
&lt;br /&gt;
Save the image in '''JPEG''' or '''PNG''' formats &lt;br /&gt;
&lt;br /&gt;
Save the image as '''PDB''' or '''Mol2''' files.&lt;br /&gt;
&lt;br /&gt;
'''Export''' the scene etc. &lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Click on '''Save Image''' option.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| For demonstration let me save the image in '''JPEG''' format.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Double click on “'''Desktop'''”.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Type the file name as '''1zik'''. &lt;br /&gt;
&lt;br /&gt;
File type as '''JPEG'''.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| Click on '''Save image''' option.&lt;br /&gt;
&lt;br /&gt;
'''Save image''' dialog box opens.&lt;br /&gt;
&lt;br /&gt;
Select the file location as '''Desktop'''.&lt;br /&gt;
&lt;br /&gt;
Type the '''File name '''as '''1zik'''. &lt;br /&gt;
&lt;br /&gt;
Choose the '''File type''' as '''JPEG'''.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Type,&lt;br /&gt;
&lt;br /&gt;
800 as image width and 600 as height.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Click on '''save''' button.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| Fix the image size according to your requirement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For demonstration, I will type 800 as width and 600 as height.&lt;br /&gt;
&lt;br /&gt;
Click on '''save''' button.&lt;br /&gt;
&lt;br /&gt;
The image is saved as '''1zik.jpg''' on the '''desktop'''.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| Cursor on the panel.&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| Let's summarize what we have learnt.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| '''Slide Number 8'''&lt;br /&gt;
&lt;br /&gt;
Summary&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| In this tutorial we typed commands to,&lt;br /&gt;
&lt;br /&gt;
* Change the '''display''' to atoms.&lt;br /&gt;
* Show and hide '''ribbons'''.&lt;br /&gt;
* Change the color of the '''amino acid residues.'''&lt;br /&gt;
* '''Label '''individual '''residues'''.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| '''Slide Number 9'''&lt;br /&gt;
&lt;br /&gt;
'''Summary'''&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| &lt;br /&gt;
&lt;br /&gt;
* Remove '''solvent '''molecules.&lt;br /&gt;
* Save the image in different file formats.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| '''Slide Number 10'''&lt;br /&gt;
&lt;br /&gt;
'''Assignment'''&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| Now for the '''Assignment'''&lt;br /&gt;
&lt;br /&gt;
Type commands to,&lt;br /&gt;
&lt;br /&gt;
* Load the structure of '''Human oxy-hemoglobin''' ('''PDB code: 2dn1''')&lt;br /&gt;
* Change the display to atoms and hide '''ribbons'''. &lt;br /&gt;
* Color all '''histidine residues''' in green.&lt;br /&gt;
* Remove the '''solvent molecules'''. &lt;br /&gt;
* Save the image in '''JPEG''' format.&lt;br /&gt;
&lt;br /&gt;
Your completed '''assignmet''' should look as follows.&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| '''Slide Number 11'''&lt;br /&gt;
&lt;br /&gt;
'''Acknowledgement '''&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| The video at the following link summarizes the Spoken Tutorial project. &lt;br /&gt;
&lt;br /&gt;
Please download and watch it. &lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| '''Slide Number 12'''&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test. &lt;br /&gt;
&lt;br /&gt;
For more details, please write to us. &lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| '''Slide number 13'''&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. &lt;br /&gt;
&lt;br /&gt;
More information on this Mission is available at the link shown&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&amp;quot;| &lt;br /&gt;
| style=&amp;quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&amp;quot;| This is Snehalatha from IIT Bombay signing off. Thank you for joining. &lt;br /&gt;
&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Snehalathak</name></author>	</entry>

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