Difference between revisions of "UCSF-Chimera/C3/Build-Structures/English-timed"
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| − | | | Let's summarize. In this tutorial, we have learnt to: create structures of small molecules, peptides | + | | | 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 | ||
Latest revision as of 12:30, 27 June 2018
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| 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. |
