Sandhya.np14 at 07:00, 27 June 2018

2018-06-27T07:00:14Z

Sandhya.np14 at 06:59, 27 June 2018

2018-06-27T06:59:00Z

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Jyotisolanki at 08:57, 7 February 2018

2018-02-07T08:57:11Z

Jyotisolanki at 09:47, 5 February 2018

2018-02-05T09:47:39Z

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

2017-11-15T09:49:52Z

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

New page

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

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

|-
| |00:05
| | In this tutorial, we will learn to :Create structures of small molecules, '''peptides''' <br/> 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 '''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
| | Hydrogens 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-membered 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 sametime click on the hydrogen.

|-
| | 05:52
| | Now the '''hydrogen'''s 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'''.'''

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| | 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.

|-
| | 07:29
| | 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 <br/> 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.

|}

@@ Line 433: / Line 433: @@
 |-
 | | 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,
 |-
 | | 09:49

@@ Line 149: / Line 149: @@
 |-
 | | 03:29
-| | Using '''Select''' menu clear the selection.
+| | Using '''Select''' menu '''clear the selection'''.
 |-

@@ Line 332: / Line 332: @@
 |-
-| | 07:29
+| | 07:26
 | | For now we will leave the phi\psi values unchanged.

UCSF-Chimera/C3/Build-Structures/English-timed - Revision history

Sandhya.np14 at 07:00, 27 June 2018

Sandhya.np14 at 06:59, 27 June 2018

Jyotisolanki at 08:57, 7 February 2018

Jyotisolanki at 09:47, 5 February 2018

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