Difference between revisions of "UCSF-Chimera/C3/Build-Structures/English-timed"

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| | In this tutorial, we will learn to :Create structures of small molecules, '''peptides''' <br/> and '''DNA''' fragments.
+
| | In this tutorial, we will learn to : create structures of small molecules, '''peptides''' <br/> and '''DNA''' fragments,
  
 
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|-
 
| |00:13
 
| |00:13
| |  Modify structure. Minimize energy, and Join models
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| |  modify structure, minimize energy and join models.
  
 
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| |00:19
 
| |00:19
| | 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.  
  
 
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| |00:30
 
| |00:30
| | 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.
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| | 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.
  
 
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| |00:48
 
| |00:48
| | Here I have opened a '''Chimera graphics window.'''  
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| | Here, I have opened a '''Chimera graphics window.'''  
  
 
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| |01:08
 
| |01:08
| | A '''Build Structure''' dialog box opens on the screen.
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| | A '''Build Structure''' dialog box opens on the '''screen'''.
  
 
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| |01:12
 
| |01:12
| | Click '''Start Structure''' button available at the top of the dialog box.
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| | Click '''Start Structure''' button, available at the top of the dialog box.
  
 
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| |01:23
 
| |01:23
| | We can also modify existing structure, adjust bonds, adjust torsions, join models etc.  
+
| | We can also modify existing structure, adjust '''bond'''s, adjust '''torsions''', join models etc.  
  
 
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| |01:41
 
| |01:41
| | We can add '''atom''', '''fragment''', fetch a structure from '''Pubchem''' data base.
+
| | We can add '''atom''', '''fragment''', fetch a structure from '''Pubchem''' data base,
  
 
|-
 
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| |01:48
 
| |01:48
| | Create '''peptide''', '''DNA''', '''RNA''' etc.  
+
| | create '''peptide''', '''DNA''', '''RNA''' etc.  
  
 
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| |01:53  
 
| |01:53  
| | To build small molecules, click on '''atom '''radio button. '''Atom parameters''' section opens.
+
| | To build small molecules, click on '''atom''' '''radio button'''. '''Atom parameters''' section opens.
  
 
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| |02:01
 
| |02:01
| | By default the structure begins with a '''helium''' atom.
+
| | By default, the structure begins with a '''helium''' atom.
  
 
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| | 02:05
 
| | 02:05
| | Click on '''Center of the view''' radio button, to place the '''helium''' atom at the center of the panel.
+
| | Click on '''Center of the view''' radio button to place the '''helium''' atom at the center of the '''panel'''.
  
 
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| |02:21
 
| |02:21
| | In '''named''' text box type the name of the session as  '''Sample1'''.  
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| | In the '''named''' text box, type the name of the session as  '''Sample1'''.  
  
 
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| | 02:57
 
| | 02:57
| | In the '''Build Structure''' dialog box;
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| | In the '''Build Structure''' dialog box,
  
 
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| | 03:00
 
| | 03:00
| | Change the element to '''carbon''', '''bonds''' to 4 and geometry to '''tetrahedral'''.
+
| | change the '''Element''' to '''Carbon''', '''Bonds''' to '''4''' and '''Geometry''' to '''tetrahedral'''.
  
 
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| | 03:08
 
| | 03:08
| | Hydrogens are attached as needed to satisfy the valency.
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| | Hydrogen atoms are attached as needed to satisfy the '''valency'''.
  
 
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| | 03:13
 
| | 03:13
| | By default some of the parameters are already selected, leave them as such.
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| | By default, some of the parameters are already selected, leave them as such.
  
 
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| | 03:29
 
| | 03:29
| | Using '''Select''' menu clear the selection.
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| | Using '''Select''' menu, clear the selection.
  
 
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| | 03:49
 
| | 03:49
| | In the '''Modify Structure''' dialog box; Change the element to '''nitrogen''', '''bonds''' to 3 , geometry '''trigonal'''.
+
| | In the '''Modify Structure''' dialog box, change the '''Element''' to '''nitrogen''', '''Bonds''' to '''3''' , '''Geometry''' -'''trigonal'''.
  
 
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| | 03:59
 
| | 03:59
| | Click on '''Apply button.'''
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| | Click on '''Apply''' button.
  
 
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| | 04:10
 
| | 04:10
| | If you want to delete any atom or bond from the structure; Select the atom or the bond, click on '''delete''' button in the '''Build Structure''' dialog box.
+
| | If you want to delete any atom or '''bond''' from the structure- select the atom or the bond, click on '''delete''' button in the '''Build Structure''' dialog box.
  
 
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| | 04:28
 
| | 04:28
| | Using the center mouse button, drag and place this model at the corner of the panel.
+
| | Using the center '''mouse''' button, drag and place this model at the corner of the panel.
  
 
|-
 
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| | 04:35
 
| | 04:35
| | In Build Structure dialog box; Click the drop-down menu and select '''Start Structure option.'''
+
| | In '''Build Structure''' dialog box, click the drop-down menu and select '''Start Structure''' option.
  
 
|-
 
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| | 04:43
 
| | 04:43
| | Now click on '''fragment '''radio''' '''button'''.'''
+
| | Now click on '''fragment '''radio button.
  
 
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| | 04:47
 
| | 04:47
| | A Fragment library of various '''cyclic '''compounds is listed here.
+
| | A '''Fragment library''' of various '''cyclic compound'''s is listed here.
  
 
|-
 
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| | 04:52
 
| | 04:52
| | Click on 5-membered rings.
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| | Click on '''5-membere rings'''.
  
 
|-
 
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| | 04:55
 
| | 04:55
| | Choose fragment from the list.
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| | Choose '''fragment''' from the list.
  
 
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| | 05:01
 
| | 05:01
| | Click on '''Apply button'''
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| | Click on '''Apply''' button.
  
 
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| | 05:13
 
| | 05:13
| | Uncheck the box for '''model number zero''' on the '''Active model''' status bar.
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| | Uncheck the box for '''model number zero''', on the '''Active model''' status bar.
  
 
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| | 05:23
 
| | 05:23
| | Using center mouse button move the '''imidazole''' closer to the '''amine model'''.
+
| | Using center '''mouse''' button, move the '''imidazole''' closer to the '''amine model'''.
  
 
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| |05:29
 
| |05:29
| We can join the two models on the panel; Using '''Join Models''' option in the Build structure dialog box.
+
| We can join the two models on the panel, using '''Join Models''' option in the '''Build structure''' dialog box.
  
 
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| | 05:37
 
| | 05:37
| | Select one '''hydrogen''' atom from each model where you intend to form a bond.
+
| | Select one hydrogen atom from each model where you intend to form a '''bond'''.
  
 
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| |05:44
 
| |05:44
| | Hold''' CTRL''' and '''Shift''' key at the sametime click on the hydrogen.
+
| | Hold''' CTRL''' and '''Shift''' key at the same time, click on the hydrogen.
  
 
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| | 05:52
 
| | 05:52
| | Now the '''hydrogen'''s are selected.
+
| | Now the hydrogens are selected.
  
 
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| | 06:03
 
| | 06:03
| | Click on '''Apply button.'''
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| | Click on '''Apply''' button.
  
 
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| |06:10  
 
| |06:10  
| | Close the '''session '''using''' File '''menu'''.'''
+
| | Close the '''session '''using''' File '''menu.
  
 
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| | 06:15
 
| | 06:15
| | Click on the '''lighting bolt icon''' at the bottom of the window; to get back to '''graphics''' window.
+
| | Click on the '''lighting bolt icon''' at the bottom of the window to get back to '''graphics''' window.
  
 
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| | 06:22
 
| | 06:22
| | Next let us create a '''peptide''' chain.  
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| | Next, let us create a '''peptide''' chain.  
  
 
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| | 06:30
 
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| | Click on '''peptide '''radio button'''.'''
+
| | Click on '''peptide '''radio button.
  
 
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| | 06:33
 
| | 06:33
| | In the '''Peptide''' '''Sequence''' text box, type the single letter code for amino acids.
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| | In the '''Peptide Sequence''' text box, type the single letter code for amino acids.
  
 
|-
 
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| | 06:39
 
| | 06:39
| | Let us type some random amino acid sequence.  
+
| | Let us type some random '''amino acid sequence'''.  
  
 
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| | 06:43
 
| | 06:43
| | Type, '''ACDEFGH''' The residues are added from N to C terminus.
+
| | Type: '''ACDEFGH'''. The '''residues''' are added from N to C terminus.
  
 
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| | 06:59
 
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| | '''Add Peptide Sequence '''dialog-box''' '''opens.
+
| | '''Add Peptide Sequence '''dialog-box opens.
  
 
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| | 07:08
 
| | 07:08
| | By default '''phi''' and '''psi''' angles of -57 and -47 are displayed.
+
| | By default, '''phi''' and '''psi''' angles of -57 and -47 are displayed.
  
 
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| | 07:15
 
| | 07:15
| | These values correspond to a '''alpha-helix '''structure''' '''for the peptide fragment'''.'''
+
| | These values correspond to a '''alpha-helix '''structure for the '''peptide fragment'''.
  
 
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| | 07:26
 
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| | For now we will leave the phi\psi values unchanged.
+
| | For now, we will leave the '''phi\psi''' values unchanged.
  
 
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| | 07:30
| | Click on OK button.
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| | Click on '''OK''' button.
  
 
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| |07:39
 
| |07:39
| | To minimize energy of the structure, type '''minimize''' on the '''command text box''' Press enter.  
+
| | To minimize energy of the structure, type: '''minimize''' on the '''command text box'''. Press '''Enter'''.  
  
 
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| | By default some parameters are selected.
+
| | By default, some parameters are selected.
  
 
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| | 07:57
 
| | 07:57
| | For now we will not make any changes. Click on '''OK''' button.
+
| | For now, we will not make any changes. Click on '''OK''' button.
  
 
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| | 08:13
 
| | 08:13
| | Observe the panel, hydrogens are added to the structure.
+
| | Observe the panel. Hydrogens are added to the structure.
  
 
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| | 08:18
 
| | 08:18
| | Another dialog box opens, choose the force field package.
+
| | Another dialog box opens. Choose the '''force field''' package.
  
 
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| | 08:24
 
| | 08:24
| | By default '''AMBER ff14SB''' is selected for standard residues.
+
| | By default, '''AMBER ff14SB''' is selected for standard residues.
  
 
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| | 08:38
 
| | 08:38
| | Now on the panel we have a structure with most preferred conformation.  
+
| | Now, on the panel, we have a structure with most preferred conformation.  
  
 
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| | 08:45
 
| | 08:45
| | Close the session using '''File '''menu and Open '''Graphics''' window.
+
| | Close the '''session''' using '''File '''menu and open '''Graphics''' window.
  
 
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| | 08:51
 
| | 08:51
| | Using the '''Build stucture''' tool, we can create a double helical DNA/RNA.  
+
| | Using the '''Build stucture''' tool, we can create a '''double helical DNA/RNA'''.  
  
 
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| |09:01
 
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| | In the '''Sequence''' text box, type one letter '''nucleotide code for a DNA fragment.'''
+
| | In the '''Sequence''' text box, type one letter '''nucleotide code''' for a DNA fragment.  
  
 
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| | 09:22
 
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| | Edit the name as '''Sample3'''
+
| | Edit the name as '''Sample3'''.
  
 
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| | Change to atoms display using presets menu.
+
| | Change to atoms display using '''Presets''' menu.
  
 
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| | 09:39
 
| | 09:39
| | Let's summarize, In this tutorial we have learnt to, Create structures of small molecules, peptides <br/> and '''DNA''' fragments.
+
| | Let's summarize. In this tutorial, we have learnt to: create structures of small molecules, peptides and '''DNA''' fragments,
+
 
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| | 09:49
 
| | 09:49
| | Modify structure.
+
| | modify structure,
  
 
|-
 
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| | 09:51
 
| | 09:51
| |  Minimize energy, and  Join models.
+
| |  minimize energy and  join models.
  
 
|-
 
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| | 09:55
 
| | 09:55
| | For the Assignment, Join two '''benzene''' molecules to build a '''biphenyl molecule'''.
+
| | For the Assignment- Join two '''benzene''' molecules to build a '''biphenyl molecule'''.
  
 
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| |  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.
  
 
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| | The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' '''Government of '''India.  
+
| | The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' Government of India.  
  
 
|-
 
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| | 10:35
 
| | 10:35
| | This is Snehalatha from IIT Bombay signing off.  
+
| | This is Snehalatha from IIT Bombay, signing off.  
 
+
 
Thank you for joining.  
 
Thank you for joining.  
  
 
|}
 
|}

Latest revision as of 12:30, 27 June 2018

Time
Narration
00:01 Welcome to this tutorial on Build Structures.
00:05 In this tutorial, we will learn to : create structures of small molecules, peptides
and DNA fragments,
00:13 modify structure, minimize energy and join models.
00:19 To follow this tutorial, you should be familiar with Chimera Interface . If not, for relevant tutorials, please visit our website.
00:30 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.
00:48 Here, I have opened a Chimera graphics window.
00:52 Let us now start building a chemical structure using Build Structure tool.
00:58 Click on Tools menu, scroll down to Structure editing option.
01:04 From the sub-menu, click on Build Structure.
01:08 A Build Structure dialog box opens on the screen.
01:12 Click Start Structure button, available at the top of the dialog box.
01:18 Here we have options to build the structure from the scratch.
01:23 We can also modify existing structure, adjust bonds, adjust torsions, join models etc.
01:33 Let's choose Start Structure option.
01:37 Here, there are many options to start a structure.
01:41 We can add atom, fragment, fetch a structure from Pubchem data base,
01:48 create peptide, DNA, RNA etc.
01:53 To build small molecules, click on atom radio button. Atom parameters section opens.
02:01 By default, the structure begins with a helium atom.
02:05 Click on Center of the view radio button to place the helium atom at the center of the panel.
02:12 We also have options to input the X , Y and Z coordinates.
02:17 Click on Select placed atom.
02:21 In the named text box, type the name of the session as Sample1.
02:26 Click on Color new atoms by element.
02:30 Click on Apply button.
02:33 A single Helium atom appears on the panel.
02:37 Now we can modify this atom to any other molecule using Modify Structure option.
02:44 Select Modify Structure option from the main drop-down menu.
02:49 Let us try to modify helium to a methane molecule.
02:53 Let the helium atom be in the selection mode.
02:57 In the Build Structure dialog box,
03:00 change the Element to Carbon, Bonds to 4 and Geometry to tetrahedral.
03:08 Hydrogen atoms are attached as needed to satisfy the valency.
03:13 By default, some of the parameters are already selected, leave them as such.
03:20 Click on Apply button.
03:23 Observe the panel. Helium atom is now replaced by Methane molecule.
03:29 Using Select menu, clear the selection.
03:33 To further modify this molecule to Methyl amine, select any hydrogen atom.
03:39 Hold the CTRL key and click on any hydrogen atom on the methane structure.
03:46 Hydrogen atom is now selected.
03:49 In the Modify Structure dialog box, change the Element to nitrogen, Bonds to 3 , Geometry -trigonal.
03:59 Click on Apply button.
04:02 Observe the panel. Amino group is now added to methane molecule.
04:07 Clear the selection using Select menu.
04:10 If you want to delete any atom or bond from the structure- select the atom or the bond, click on delete button in the Build Structure dialog box.
04:22 To revert back to the original structure, add hydrogens using Tools menu.
04:28 Using the center mouse button, drag and place this model at the corner of the panel.
04:35 In Build Structure dialog box, click the drop-down menu and select Start Structure option.
04:43 Now click on fragment radio button.
04:47 A Fragment library of various cyclic compounds is listed here.
04:52 Click on 5-membere rings.
04:55 Choose fragment from the list.
04:58 I will choose imidazole.
05:01 Click on Apply button.
05:04 Imidazole molecule is displayed on the screen.
05:09 Move the imidazole molecule closer to methyl amine model.
05:13 Uncheck the box for model number zero, on the Active model status bar.
05:19 This will make the amine model inactive on screen.
05:23 Using center mouse button, move the imidazole closer to the amine model.
05:29 We can join the two models on the panel, using Join Models option in the Build structure dialog box.
05:37 Select one hydrogen atom from each model where you intend to form a bond.
05:44 Hold CTRL and Shift key at the same time, click on the hydrogen.
05:52 Now the hydrogens are selected.
05:55 Click on other bond option.
05:58 Information regarding the bonds is displayed on the dialog box.
06:03 Click on Apply button.
06:05 Observe the panel, two models are joined.
06:10 Close the session using File menu.
06:15 Click on the lighting bolt icon at the bottom of the window to get back to graphics window.
06:22 Next, let us create a peptide chain.
06:25 In the Build Structure dialog box, select Start Structure.
06:30 Click on peptide radio button.
06:33 In the Peptide Sequence text box, type the single letter code for amino acids.
06:39 Let us type some random amino acid sequence.
06:43 Type: ACDEFGH. The residues are added from N to C terminus.
06:52 Type session name as Sample2.
06:56 Click on Apply button.
06:59 Add Peptide Sequence dialog-box opens.
07:03 This dialog box is for specifying phi and psi angles.
07:08 By default, phi and psi angles of -57 and -47 are displayed.
07:15 These values correspond to a alpha-helix structure for the peptide fragment.
07:21 If you want to set the values, you can do so manually.
07:26 For now, we will leave the phi\psi values unchanged.
07:30 Click on OK button.
07:33 Observe the panel. We have a peptide chain displayed as helix.
07:39 To minimize energy of the structure, type: minimize on the command text box. Press Enter.
07:48 A Dock Prep dialog box appears, with model name.
07:53 By default, some parameters are selected.
07:57 For now, we will not make any changes. Click on OK button.
08:02 This opens another dialog box to add hydrogens to the structure.
08:07 A few parameters are already selected. Click on OK button.
08:13 Observe the panel. Hydrogens are added to the structure.
08:18 Another dialog box opens. Choose the force field package.
08:24 By default, AMBER ff14SB is selected for standard residues.
08:31 Click on OK button.
08:34 It will take a few seconds to minimize the structure.
08:38 Now, on the panel, we have a structure with most preferred conformation.
08:45 Close the session using File menu and open Graphics window.
08:51 Using the Build stucture tool, we can create a double helical DNA/RNA.
08:57 Click on the radio button helical DNA/RNA.
09:01 In the Sequence text box, type one letter nucleotide code for a DNA fragment.
09:08 For demonstration I will type, ATGCATGC.
09:16 Click on DNA, click on B-form.
09:22 Edit the name as Sample3.
09:25 Click on Apply button.
09:28 A model of DNA as double helix displayed on the panel.
09:34 Change to atoms display using Presets menu.
09:39 Let's summarize. In this tutorial, we have learnt to: create structures of small molecules, peptides and DNA fragments,
09:49 modify structure,
09:51 minimize energy and join models.
09:55 For the Assignment- Join two benzene molecules to build a biphenyl molecule.
10:02 Build a peptide fragment with your own choice of amino acid sequence.
10:08 Build a RNA fragment with a random nucleotide sequence.
10:13 This video summarizes the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it.
10:21 We conduct workshops using Spoken Tutorials and give certificates. Please contact us.
10:28 The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
10:35 This is Snehalatha from IIT Bombay, signing off.

Thank you for joining.

Contributors and Content Editors

Jyotisolanki, Sandhya.np14