Difference between revisions of "UCSF-Chimera/C3/Build-Structures/English-timed"
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− | | | In this tutorial, we will learn to : | + | | | 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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| |00:19 | | |00:19 | ||
− | | | To follow this tutorial you should be familiar with | + | | | 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''' | + | | | 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.''' | + | | | 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. | + | | | 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. | + | | | 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 | + | | | 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. |
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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 | + | | | 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'''. | + | | | 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 | + | | | 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'''. |
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| | 03:08 | | | 03:08 | ||
− | | | | + | | | 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. | + | | | By default, some of the parameters are already selected, leave them as such. |
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| | 03:29 | | | 03:29 | ||
− | | | Using '''Select''' menu | + | | | Using '''Select''' menu, clear the selection. |
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| | 03:49 | | | 03:49 | ||
− | | | In the '''Modify Structure''' dialog box | + | | | 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 | + | | | Click on '''Apply''' button. |
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| | 04:10 | | | 04:10 | ||
− | | | If you want to delete any atom or bond from the structure | + | | | 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 | + | | | 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 | + | | | Now click on '''fragment '''radio button. |
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| | 04:47 | | | 04:47 | ||
− | | | A Fragment library of various '''cyclic ''' | + | | | A '''Fragment library''' of various '''cyclic compound'''s is listed here. |
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| | 04:52 | | | 04:52 | ||
− | | | Click on 5- | + | | | Click on '''5-membere rings'''. |
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| | 04:55 | | | 04:55 | ||
− | | | Choose fragment from the list. | + | | | Choose '''fragment''' from the list. |
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| | 05:01 | | | 05:01 | ||
− | | | Click on '''Apply | + | | | 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. | + | | | 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 | + | | 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 | + | | | 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 | + | | | Hold''' CTRL''' and '''Shift''' key at the same time, click on the hydrogen. |
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| | 05:52 | | | 05:52 | ||
− | | | Now the | + | | | Now the hydrogens are selected. |
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| | 06:03 | | | 06:03 | ||
− | | | Click on '''Apply | + | | | 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 | + | | | 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. | + | | | Next, let us create a '''peptide''' chain. |
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| | 06:30 | | | 06:30 | ||
− | | | Click on '''peptide '''radio button | + | | | Click on '''peptide '''radio button. |
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| | 06:33 | | | 06:33 | ||
− | | | In the '''Peptide | + | | | 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 | + | | | Type: '''ACDEFGH'''. The '''residues''' are added from N to C terminus. |
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| | 06:59 | | | 06:59 | ||
− | | | '''Add Peptide Sequence '''dialog-box | + | | | '''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''' | + | | | These values correspond to a '''alpha-helix '''structure for the '''peptide fragment'''. |
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| | 07:26 | | | 07:26 | ||
− | | | 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 | | | 07:30 | ||
− | | | Click on OK button. | + | | | 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 | + | | | To minimize energy of the structure, type: '''minimize''' on the '''command text box'''. Press '''Enter'''. |
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| | 07:53 | | | 07:53 | ||
− | | | 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 | + | | | Observe the panel. Hydrogens are added to the structure. |
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| | 08:18 | | | 08:18 | ||
− | | | Another dialog box opens | + | | | 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 | + | | | 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 | | |09:01 | ||
− | | | 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 | | | 09:22 | ||
− | | | Edit the name as '''Sample3''' | + | | | Edit the name as '''Sample3'''. |
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| | 09:34 | | | 09:34 | ||
− | | | Change to atoms display using | + | | | Change to atoms display using '''Presets''' menu. |
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| | 09:39 | | | 09:39 | ||
− | | | Let's summarize | + | | | 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, |
|- | |- | ||
| | 09:51 | | | 09:51 | ||
− | | | | + | | | minimize energy and join models. |
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| | 09:55 | | | 09:55 | ||
− | | | For the Assignment | + | | | For the Assignment- Join two '''benzene''' molecules to build a '''biphenyl molecule'''. |
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| | 10:13 | | | 10:13 | ||
− | | | 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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| |10:28 | | |10:28 | ||
− | | | The Spoken Tutorial Project is funded by '''NMEICT, MHRD | + | | | 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
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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. |