UCSF-Chimera/C4/Attributes/English-timed - Revision history

Sandhya.np14 at 10:46, 28 June 2018

2018-06-28T10:46:37Z

Sandhya.np14 at 09:55, 28 June 2018

2018-06-28T09:55:50Z

Jyotisolanki: Created page with "{| border=1 | Time | Narration |- |00:01 | Welcome to this tutorial on '''Attributes.''' |- |00:05 | In this tutorial we will learn to, Ch..."

2017-12-13T07:41:03Z

Created page with "{| border=1 | <center>Time</center> | <center>Narration</center> |- |00:01 | Welcome to this tutorial on '''Attributes.''' |- |00:05 | In this tutorial we will learn to, Ch..."

New page

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

|-
|00:01
| Welcome to this tutorial on '''Attributes.'''

|-
|00:05
| In this tutorial we will learn to, Change '''attributes''' of atoms, residues and models.

|-
|00:13
| Color atoms in a protein according to '''B-factor''' values.

|-
|00:18
|Color residues according to '''kdhydrophobicity''' values.

|-
|00:24
| To follow this tutorial you should be familiar with '''Chimera''' interface . If not, for relevant tutorials, please visit our website.

|-
|00:33
| To record this tutorial I am using '''Ubuntu''' OS version. 14.04 , '''Chimera''' version 1.10.2 , '''Mozilla Firefox''' browser 42.0 ,And a working Internet connection.

|-
|00:50
| Here I have opened a '''Chimera''' window.

|-
|00:54
|Using command line open the structure of '''Leucine zipper. '''

|-
| 00:52
|On the command text box, type, '''open 1zik''' Press '''Enter'''.

|-
|01:05
| The model on the panel is shown as '''ribbons'''.

|-
|01:10
|Using '''Presets''' menu, change the display to '''Interactive 2''' '''. '''

|-
|01:14
| To hide water molecules, on the '''command line''' type, '''delete solvent'''. Press '''Enter'''.

|-
|01:22
| To change the display to sticks, type, '''rep stick''' , Press '''Enter'''.

|-
|01:30
| Add hydrogens to the structure, type, '''addh '''

|-
|01:36
| Now let us learn how to change the '''attributes '''of '''atoms and residues''' for this structure.

|-
|01:43
| '''Attributes ''' are properties with names and values.

|-
|01:47
|In '''Chimera''', items such as '''atoms, bonds, residues''' and '''molecule models''' have '''Attributes.'''

|-
|01:54
| There are different ways to change the '''Attributes'''.

|-
|01:57
| Open the '''Model Panel''' using '''Favorites''' menu.

|-
|02:01
| '''Model Panel''' dialog box appears on the screen.

|-
|02:05
|Click on the '''attributes''' button on the right side of the panel.

|-
|02:10
|'''Attributes''' dialog box for '''1zik''' opens on the screen.

|-
|02:15
|The dialog box has '''attribute''' list.

|-
|02:18
| The list includes. '''Molecule Attributes''' and its components, '''Atom, bond '''and''' residue attributes.'''

|-
|02:28
|Select''' Molecule Attributes.'''

|-
|02:31
| The available '''attributes''' are listed on the window.

|-
|02:35
| For example - To change the display of aromatic rings, click on the button next to '''aromatic display'''.

|-
|02:42
|Select '''True''' from the drop-down.

|-
|02:45
| Select '''Aromatic ring style''' as '''disk'''.

|-
|02:49
|Click on the '''color well''' next to aromatic color.

|-
|02:53
|Select color from the '''color editor'''.

|-
|02:56
|Close the dialog box.

|-
|02:59
| Observe the panel. All the '''aromatic rings''' are shown with disks in the center.

|-
|03:06
| Change the display of the structure to '''ball and stick'''.

|-
|03:10
|On the command line, type, '''rep bs'''

|-
|03:16
| On the attributes dialog box, change the Van der Walls radii of the atoms.

|-
|03:22
|Change the value of '''ball scale''' to 0.5. Press '''Enter'''.

|-
|03:27
| Observe the panel. The atoms are shown with larger atomic radii.

|-
|03:33
| Again click on '''Molecular Attributes '''check box.

|-
|03:38
|From the list, click on '''Component Atom Attributes'''.

|-
|03:43
| In the corresponding window, click on '''atom style button''' .

|-
|03:48
|The drop-down menu has many options.

|-
|03:51
|Click on''' sphere''' to change the display to '''cpk'''.

|-
|03:55
|Observe the panel.

|-
|03:57
|Select '''dot''' to bring back the '''sticks''' display.

|-
|04:02
| Now click on '''Component Bond Attributes.'''

|-
|04:10
|Here, there are options to change bond style to '''stick''' or '''wire'''.

|-
|04:13
| Click on '''Component Residue Attributes.'''

|-
|04:17
|Here we have options to change the attributes of the ribbon.

|-
|04:22
| Using '''presets''' menu, change the display of the structure on the panel to '''ribbons'''.
|-
|04:28
|Now Clicking the '''Attribute''' dialog-box.

|-
|04:32
| Now,in the '''Attribute''' dialog-box, click on the '''color well '''next to '''ribbon color'''. Select a ribbon color.

|-
|04:41
|And click on '''close''' option to close the '''color editor'''.

|-
|04:46
| There are options to change the cross-section of the '''ribbon''' and '''scaling'''.

|-
|04:52
|Close the dialog box.

|-
|04:55
| Again, change the display to '''atoms '''using '''Presets '''menu.

|-
|05:00
| '''Attributes''' can also be changed using '''Tools''' menu.

|-
|05:03
| Click on '''Tools''' menu, scroll down to '''Structure Analysis'''.

|-
|05:09
|And select '''Render by Attribute '''option from the sub-menu.

|-
|05:14
| '''Render by attribute''' dialog box opens.

|-
|05:17
| Here we have options to change the '''attributes '''of '''atoms, residues, molecules, segmentation regions''' etc.

|-
|05:27
|Select '''atoms.''' Click on''' Render.'''

|-
|05:32
| Click on '''Attribute''' list to check for available options.

|-
|05:37
|The list shows two options: '''bfactor''' and '''occupancy'''

|-
|05:43
|These two '''attributes''' can be read from the input '''PDB''' file.

|-
|05:48
| Choose '''bfactor.'''

|-
|05:50
|A '''histogram''' of values will appear, with colored vertical bars.

|-
|05:55
| '''B-factor''' values are a measure of mobility in the '''macromolecule'''.

|-
|06:01
| '''Atoms''' with low '''B-factor''' values belong to a part of the structure that is well ordered.

|-
|06:08
|Atoms with large '''B-factor''' values belong to part of the structure that is very flexible.

|-
|06:15
| PDB file for a '''protein''' structure contains B-factor information.

|-
|06:21
|Back to the panel.

|-
|06:23
|The vertical bars can be dragged along the '''histogram''' with the mouse.

|-
|06:29
|The value of B-factor is displayed in the ''' Value ''' text box.

|-
|06:34
|Drag the blue vertical bar to zero, red to 100.

|-
|06:41
|Then fix the white bar at value 50.

|-
|06:45
|Click on '''Colors''' button.

|-
|06:48
|Check options for '''color atoms''', '''keep opaque''' and '''color surfaces.'''

|-
|06:55
|The default color '''palette''' is blue and red.

|-
|06:59
|You can change the color '''palette''', using drop-down menu.

|-
|07:04
| Click on '''Apply''' button.

|-
|07:07
| Observe the panel. '''Atoms''' with high '''B-factor''' values are shown in red and least in blue.

|-
|07:16
| As expected, '''atoms''' with high '''B-factors''' are on the outside of the structure.

|-
|07:22
| Now let us change the '''attributes''' of '''Residues'''.

|-
|07:26
| In the '''Select by Attribute''' dialog box, click on '''Attributes button.'''

|-
|07:32
|From the drop-down, select '''residues'''.

|-
|07:36
| Click on '''Render.'''

|-
|07:38
|The '''attributes''' for '''residues''' include '''kdHydrophobicity scale'''.

|-
|07:44
| Click on '''kdHydrophobicity''' from the drop-down menu.

|-
|07:48
|The values are displayed in the histogram.

|-
|07:52
|'''kdHydrophobicity scales''' are values that define relative '''hydrophobicity''' of '''amino acid residues'''.

|-
|08:00
| '''KdHydrophobicity''' values are positive for '''hydrophobic residues''' and Negative values for '''polar residues'''.

|-
|08:09
| '''Hydrophobicity''' of the '''residues''' can be shown with colors or worms.

|-
|08:15
|Choose '''Colors'''. By default, some of the parameters are selected.

|-
|08:21
|Click on '''Apply''' button. Observe the panel.

|-
|08:26
|The '''hydrophobic residues''' are colored in red, and '''polar residues''' are colored in blue.

|-
|08:33
| Click on '''Worms''' button. Click on '''Apply'''.

|-
|08:38
|Observe the panel.

|-
|08:41
|'''Worms''' are modified ribbons that vary in radius.

|-
| 08:47
| Most '''hydrophobic residues''' face the interior of the structure.

|-
|08:52
| By default, the more '''hydrophobic residues''' will be shown with larger radius.

|-
|09:00
| To return the structure to normal '''ribbon''':

|-
|09:03
|Click on worm-style button and choose '''non-worm''' option.

|-
|09:09
|Click on '''OK '''button.

|-
|09:12
| Close the '''Chimera''' session using '''File''' menu.

|-
|09:16
| Let's summarize, In this tutorial we have learnt to, Change '''attributes''' of '''atoms, residues '''and''' models.'''

|-
|09:25
|Color '''atoms''' in a '''protein''' according to '''B-factor''' values.

|-
|09:30
| Color '''residues''' according to '''kdHydrophobicity '''values.

|-
|09:35
| As an '''Assignment,''' Open a model of '''hemoglobin (PDB code: 2HCO)''' on the panel. Color the atoms according to '''B-factor''' values.

|-
|09:44
|Color the residues according to '''kdHydrophobicity '''values.

|-
|09:49
| This video summarizes the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it.

|-
|09:56
| We conduct workshops using Spoken Tutorials and give certificates.Please contact us.

|-
|10:04
| The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' '''Government of '''India.

|-
|10:10
| This is Snehalatha from IIT Bombay signing off.
Thank you for joining.

|}

@@ Line 141: / Line 141: @@
 |-
 |03:10
-|On the command line, type, '''rep bs'''
+|On the '''command line''', type: '''rep bs'''
 |-
 |03:16
-| On the attributes dialog box, change the Van der Walls radii of the atoms.
+| On the '''attributes''' dialog box, change the '''Van der Walls''' radii of the atoms.
 |-
 |03:22
-|Change the value of '''ball scale''' to 0.5. Press '''Enter'''.
+|Change the value of '''ball scale''' to '''0.5'''. Press '''Enter'''.
 |-
@@ Line 165: / Line 165: @@
 |-
 |03:43
-| In the corresponding window, click on '''atom style button''' .
+| In the corresponding window, click on '''atom style''' button .
 |-
@@ Line 197: / Line 197: @@
 |-
 |04:17
-|Here we have options to change the attributes of the ribbon.
+|Here we have options to change the attributes of the '''ribbon'''.
 |-
 |04:22
-| Using '''presets''' menu, change the display of the structure on the panel to '''ribbons'''.
+| Using '''Presets''' menu, change the display of the structure on the panel to '''ribbons'''.
 |-
 |04:28
-|Now Clicking the '''Attribute''' dialog-box.
+|Now clicking the '''Attribute''' dialog-box.
 |-
 |04:32
-| Now,in the '''Attribute''' dialog-box, click on the '''color well '''next to '''ribbon color'''.  Select a ribbon color.
+| Now, in the '''Attribute''' dialog-box, click on the '''color well '''next to '''ribbon color'''.  Select a ribbon color.
 |-
@@ Line 268: / Line 268: @@
 |-
 |05:50
-|A '''histogram''' of values will appear, with colored vertical bars.
+|A '''histogram''' of values will appear  with colored vertical bars.
 |-
@@ Line 276: / Line 276: @@
 |-
 |06:01
-| '''Atoms''' with low '''B-factor''' values belong to a part of the structure that is well ordered.
+| Atoms with low '''B-factor''' values belong to a part of the structure that is well ordered.
 |-
@@ Line 284: / Line 284: @@
 |-
 |06:15
-| PDB file for a '''protein''' structure contains B-factor information.
+| '''PDB file''' for a '''protein''' structure contains B-factor information.
 |-
@@ Line 292: / Line 292: @@
 |-
 |06:23
-|The vertical bars can be dragged along the '''histogram''' with the mouse.
+|The vertical bars can be dragged along the '''histogram''' with the '''mouse'''.
 |-
@@ Line 316: / Line 316: @@
 |-
 |06:55
-|The default color '''palette''' is blue and red.
+|The '''default''' color '''palette''' is blue and red.
 |-
@@ Line 328: / Line 328: @@
 |-
 |07:07
-| Observe the panel. '''Atoms''' with high '''B-factor''' values are shown in red and least in blue.
+| Observe the panel. Atoms with high '''B-factor''' values are shown in red and least in blue.
 |-
 |07:16
-| As expected, '''atoms''' with high '''B-factors''' are on the outside of the structure.
+| As expected, atoms with high '''B-factors''' are on the outside of the structure.
 |-
 |07:22
-| Now let us change the '''attributes''' of '''Residues'''.
+| Now, let us change the '''attributes''' of '''Residues'''.
 |-
 |07:26
-| In the '''Select by Attribute''' dialog box, click on '''Attributes button.'''
+| In the '''Select by Attribute''' dialog box, click on '''Attributes''' button.
 |-
@@ Line 360: / Line 360: @@
 |-
 |07:48
-|The values are displayed in the histogram.
+|The values are displayed in the '''histogram'''.
 |-
@@ Line 396: / Line 396: @@
 |-
 |08:41
-|'''Worms''' are modified ribbons that vary in radius.
+|'''Worms''' are modified '''ribbon'''s that vary in radius.
 |-
@@ Line 412: / Line 412: @@
 |-
 |09:03
-|Click on worm-style button and choose '''non-worm''' option.
+|click on '''worm-style''' button and choose '''non-worm''' option.
 |-
@@ Line 424: / Line 424: @@
 |-
 |09:16
-| Let's summarize, In this tutorial we have learnt to,  Change '''attributes''' of '''atoms, residues '''and''' models.'''
+| Let's summarize, In this tutorial, we have learnt to: change '''attributes''' of '''atoms, residues '''and''' models,'''
 |-
 |09:25
-|Color '''atoms''' in a '''protein''' according to '''B-factor''' values.
+|color atoms in a '''protein''' according to '''B-factor''' values,
 |-
 |09:30
-| Color '''residues''' according to '''kdHydrophobicity '''values.
+| color '''residues''' according to '''kdHydrophobicity '''values.
 |-
 |09:35
-| As an '''Assignment,'''  Open a model of '''hemoglobin (PDB code: 2HCO)''' on the panel. Color the atoms according to '''B-factor''' values.
+| As an '''assignment,'''  Open a model of '''hemoglobin (PDB code: 2HCO)''' on the panel. Color the atoms according to '''B-factor''' values.
 |-
@@ Line 444: / Line 444: @@
 |-
 |09:49
-| This video summarizes the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it.
+| This video summarizes the '''Spoken Tutorial''' project. If you do not have good bandwidth, you can download and watch it.
 |-
 |09:56
-|  We conduct workshops using Spoken Tutorials and give certificates.Please contact us.
+|  We conduct workshops using Spoken Tutorials and give certificates. Please contact us.
 |-
 |10:04
-| The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' '''Government of '''India.
+| The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' Government of India.
 |-
 |10:10
-| This is Snehalatha from IIT Bombay signing off.
+| This is Snehalatha from IIT Bombay, signing off.
 Thank you for joining.
 |}

@@ Line 9: / Line 9: @@
 |-
 |00:05
-| In this tutorial we will learn to, Change '''attributes''' of atoms, residues and models.
+| In this tutorial, we will learn to: change '''attributes''' of atoms, residues and models,
 |-
 |00:13
-| Color atoms in a protein according to '''B-factor''' values.
+| color atoms in a protein according to '''B-factor''' values,
 |-
 |00:18
-|Color residues according to '''kdhydrophobicity''' values.
+|color residues according to '''kdhydrophobicity''' values.
 |-
 |00:24
-| To follow this tutorial you should be familiar with '''Chimera''' interface . If not, for relevant tutorials, please visit our website.
+| To follow this tutorial, you should be familiar with '''Chimera''' interface . If not, for relevant tutorials, please visit our '''website'''.
 |-
 |00:33
-| To record this tutorial I am using '''Ubuntu''' OS version. 14.04 , '''Chimera''' version 1.10.2 , '''Mozilla Firefox''' browser 42.0 ,And a working Internet connection.
+| To record this tutorial, I am using '''Ubuntu OS''' version '''14.04''', '''Chimera''' version '''1.10.2''' , '''Mozilla Firefox''' browser '''42.0'''  and a working '''internet''' connection.
 |-
 |00:50
-| Here I have opened a '''Chimera''' window.
+| Here, I have opened a '''Chimera''' window.
 |-
 |00:54
-|Using command line open the structure of '''Leucine zipper. '''
+|Using '''command line''', open the structure of '''Leucine zipper. '''
 |-
 | 00:52
-|On the command text box, type, '''open 1zik'''  Press '''Enter'''.
+|On the '''command''' text box, type:, '''open 1zik'''.  Press '''Enter'''.
 |-
 |01:05
-| The model on the panel is shown as '''ribbons'''.
+| The model on the '''panel''' is shown as '''ribbons'''.
 |-
 |01:10
-|Using '''Presets''' menu, change the display to '''Interactive 2''' '''. '''
+|Using '''Presets''' menu, change the display to '''Interactive 2''' .
 |-
 |01:14
-| To hide water molecules, on the '''command line''' type,  '''delete solvent'''. Press '''Enter'''.
+| To hide water molecules, on the '''command line''' type:  '''delete solvent'''. Press '''Enter'''.
 |-
 |01:22
-| To change the display to sticks, type, '''rep stick''' , Press '''Enter'''.
+| To change the display to '''sticks''', type: '''rep stick'''. Press '''Enter'''.
 |-
 |01:30
-| Add hydrogens to the structure, type, '''addh '''
+| Add hydrogens to the structure, type: '''addh '''.
 |-
 |01:36
-| Now let us learn how to change the '''attributes '''of '''atoms and residues''' for this structure.
+| Now, let us learn how to change the '''attributes '''of atoms and '''residues''' for this structure.
 |-
@@ Line 69: / Line 69: @@
 |-
 |01:47
-|In '''Chimera''', items such as '''atoms, bonds, residues''' and '''molecule models''' have '''Attributes.'''
+|In '''Chimera''', items such as '''atoms, bonds, residues''' and molecule models have '''Attributes.'''
 |-
@@ Line 81: / Line 81: @@
 |-
 |02:01
-| '''Model Panel''' dialog box appears on the screen.
+| '''Model Panel''' dialog box appears on the '''screen'''.
 |-
@@ Line 97: / Line 97: @@
 |-
 |02:18
-| The list includes. '''Molecule Attributes''' and its components, '''Atom, bond '''and''' residue attributes.'''
+| The list includes '''Molecule Attributes''' and its components- '''Atom, bond '''and''' residue attributes.'''
 |-
@@ Line 133: / Line 133: @@
 |-
 |02:59
-| Observe the panel. All the '''aromatic rings''' are shown with disks in the center.
+| Observe the panel. All the '''aromatic rings''' are shown with '''disk'''s in the center.
 |-