Sandhya.np14 at 07:09, 26 June 2018

2018-06-26T07:09:39Z

PoojaMoolya: Created page with "{| border=1 ! Time ! Narration |- | 00:01 |Welcome to this tutorial on '''Writing Commands '''in '''Chimera'''. |- | 00:06 |In this tutoria..."

2017-11-02T11:50:25Z

Created page with "{| border=1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 |Welcome to this tutorial on '''Writing Commands '''in '''Chimera'''. |- | 00:06 |In this tutoria..."

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{| border=1
! <center>Time</center>
! <center>Narration</center>

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| 00:01
|Welcome to this tutorial on '''Writing Commands '''in '''Chimera'''.

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| 00:06
|In this tutorial, we will type commands to- Change the '''display''' to atoms.

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| 00:12
| Show and hide '''ribbons'''.

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| 00:14
| Change the color of the '''amino acid residues.'''

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| 00:18
| Label individual '''residues'''.

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| 00:21
| Remove '''solvent''' molecules. And save the image in different file formats.

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| 00:28
|To follow this tutorial you should have knowledge of- Undergraduate '''Biochemistry'''

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| 00:34
| Must be familiar with, '''Structural Biology ''' and '''Chimera interface'''.

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| 00:40
| For relevant tutorials, please visit our website.

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| 00:44
|To record this tutorial, I am using '''Ubuntu OS version''' 14.04

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| 00:50
| '''Chimera''' '''version''' 1.10.2

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| 00:53
| '''Mozilla firefox browser''' 42.0 And a working '''Internet connection'''.

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| 01:00
|Double-click on the '''Chimera''' icon to open the '''Chimera''' window.

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| 01:06
|Click on the '''lightning bolt icon''' to open the '''graphics window'''.

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| 01:10
|In this tutorial, I will demonstrate how to use '''commands''' to manipulate the structure.

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| 01:16
| Open the '''Command Line''' using '''Favorites''' menu.

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| 01:20
|A '''command text box''' appears at the bottom of the '''Chimera''' window.

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| 01:25
|Tasks performed with '''menus '''can be carried out using '''commands'''.

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| 01:31
|About '''Chimera Commands'''.

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| 01:34
|'''Chimera commands''' are entered at the''' Command line.'''

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| 01:38
|Multiple '''commands '''can be combined into one line with '''semicolon''' separators.

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| 01:43
|Press '''Enter key''' to execute the '''command'''.

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| 01:47
|Previous '''commands''' can be accessed from '''command History.'''

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| 01:51
|More information about '''commands''' is given at the link shown.

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| 01:56
|Back to the '''Chimera''' '''window'''. Let us open a model of '''leucine zipper''' by typing a '''command'''.

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| 02:03
|The '''command''' starts with a '''command''' word.

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| 02:06
|On the '''command line''' text box, type- '''open space 1zik'''.

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| 02:13
|You need a working '''Internet connection''' for this step.

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| 02:17
|Press''' Enter''' to execute the '''command'''.

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| 02:20
|The structure appears on the screen.

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| 02:23
|To change the '''ribbons''' display to '''atoms''', in the '''command line text box''' type: The''' command '''word''' display '''. Press '''Enter'''.

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| 02:34
|We now have the structure of the '''protein''' in '''atoms display'''.

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| 02:38
|The structure is partially represented as '''ribbons'''.

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| 02:42
|To hide the '''ribbons'''- Type, the '''wave symbol''', also known as '''tilda, ''' followed by the '''command''' word '''ribbon.'''

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| 02:51
|A '''command''' with a '''tilda''' indicates the reverse function.

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| 02:55
|Here, '''tilda''' symbol followed by''' ribbon keyword''' hides the '''ribbons'''.
Press '''Enter'''.

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|03:03
|We can use '''color command''' to set colors to '''atoms, bonds, surfaces''' etc.

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| 03:10
|For example, to change the color of all '''leucines''', type:

'''Color space yellow space colon''' followed by the three letter abreviation for the '''amino acid'''.

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| 03:24
|For '''leucine''', I will type '''leu'''.

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| 03:28
|Here '''color''' is '''command word''' with '''argument''' as '''yellow''' and the target is all''' leucines''' in the structure.

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| 03:37
|If you do not specify a target, the entire structure will be colored in yellow.

Press '''Enter'''.

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| 03:45
|Observe the '''panel'''. All the '''leucines''' are now colored yellow.

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| 03:51
|We can specifically color an '''amino acid''' present at a particular location.

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| 03:56
|For example to change the color of''' histidine,''' present at position 18 on '''chain B''', type -

'''color space red space colon18.B'''. Press '''Enter'''.

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| 04:13
|Observe the panel. '''histidine''' is now colored in''' red'''.

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| 04:19
|To change the display of the entire structure to '''CPK spacefill''', type '''rep '''

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| 04:26
|'''rep''' is the truncated version for the keyword '''represent'''. '''rep space sphere''' ; press '''Enter'''.

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| 04:37
|Observe the panel.

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| 04:39
|To bring back the structure to '''stick''' display, again type '''rep space stick'''

Press''' Enter'''

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| 04:50
|To hide the''' solvent''' molecules from the structure, type - '''del''' (for delete) '''space solvent'''

Press '''Enter'''.

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| 05:02
|To activate '''residues''' for selection, use '''select command''' word.

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| 05:08
|On the '''command line''' text box type, '''select space colon '''followed by the number and '''chain''' of the residue.

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| 05:18
|For example to activate the '''lysine''' present at the position 28, on''' chain B''' Type,'''select space colon '''followed by''' 28 dot B '''. Press '''Enter'''.

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| 05:34
|Now to show the '''label''' for the '''residue''' selected, type '''rlabel space sel'''

Press '''Enter'''.

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| 05:44
|Observe the panel. The '''residue label''' for the selected '''residue''' is displayed.

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| 05:51
|To de-select the '''residue''' which we have selected earlier, press up arrow key to get the '''select command'''.

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| 05:59
|Type the '''tilda symbol''' at the beginning of the '''command'''. Press '''Enter'''.

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| 06:05
|A list of '''keywords''' and '''command index''' is available in the '''Help menu'''.

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| 06:09
|Click on the '''Help menu''', scroll down and click on '''Commands index'''.

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| 06:16
|A '''web-page '''opens with the list of '''keywords''' to write '''commands'''.

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| 06:22
|Back to the '''Chimera''' window.

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| 06:25
|If you want to change the background color from black to blue, type: '''background space solid space blue'''

Press '''Enter'''.

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| 06:38
|The panel is now blue in color.

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| 06:41
|To view the '''Command''' history, click on the black triangle present at the right side of the '''Command line'''.

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| 06:48
|The '''Command history''' lists previously used '''commands.'''

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| 06:53
|'''Commands''' can be re-executed by clicking on the '''command'''.

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| 06:57
|To hide the '''command line''', click on '''Hide command line''' option in the drop down.

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| 07:03
|There are many options to '''save '''the structure you have created. Open the '''File menu.'''

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| 07:09
|You can: '''Restore a Session''', '''Save a Session'''

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| 07:14
|Save the image in '''JPEG''' or '''PNG''' formats

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| 07:19
|Save the image as '''PDB''' or '''Mol2''' files, '''Export''' the scene etc.

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| 07:27
|For demonstration, let me save the image in '''JPEG''' format.

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|07:33
|Click on '''Save image''' option. A '''Save image''' dialog box opens.

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| 07:40
|Select the file location as '''Desktop'''.

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| 07:44
|Type the '''File name '''as '''1zik'''. Choose the '''File type''' as '''JPEG'''.

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| 07:52
|Fix the image size according to your requirement.

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| 07:56
|For demonstration, I will type 800 as width and 600 as height.

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| 08:05
|Click on '''Save''' button. The image is saved as '''1zik.jpg''' on the '''Desktop'''.

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| 08:15
|Let's summarize what we have learnt.

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|08:17
|In this tutorial we typed '''commands''' to, Change the '''display''' to '''atoms'''.

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| 08:22
| Show and hide '''ribbons'''.

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| 08:25
| Change the color of the '''amino acid residues.'''

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| 08:28
| '''Label '''individual '''residues'''.

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| 08:31
|Remove '''solvent molecules'''. Save the image in different file formats.

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|08:38
|Now for the '''Assignment'''

Type '''commands''' to, Load the structure of '''Human oxy-hemoglobin''' ('''PDB code: 2dn1''')

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| 08:48
| Change the display to '''atoms''' and hide '''ribbons'''.

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| 08:52
| Color all '''histidine residues''' in green.

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| 08:56
| Remove the '''solvent molecules''' and Save the image in '''JPEG''' format.

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| 09:03
|Your completed '''assignment''' should look as follows.

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| 09:12
|The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

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| 09:19
|The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.

For more details, please write to us.

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|09:29
|Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

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| 09:35
|More information on this Mission is available at the link shown.

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| 09:40
|This is Snehalatha from IIT Bombay signing off. Thank you for joining.

|}

UCSF-Chimera/C2/Writing-Commands/English-timed - Revision history

Sandhya.np14 at 07:09, 26 June 2018

PoojaMoolya: Created page with "{| border=1 ! Time ! Narration |- | 00:01 |Welcome to this tutorial on '''Writing Commands '''in '''Chimera'''. |- | 00:06 |In this tutoria..."