Difference between revisions of "UCSF-Chimera/C3/Structure-Analysis/English-timed"
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| | 00:05 | | | 00:05 | ||
− | | | In this tutorial, we will learn to : | + | | | In this tutorial, we will learn to : measure distance between atoms in the structure, show Hydrogen '''bond'''s, identify non-polar interactions, |
|- | |- | ||
| | 00:16 | | | 00:16 | ||
− | | | + | | and rotate bonds in the '''residues''' to get different '''rotamers'''. |
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| | 00:21 | | | 00:21 | ||
− | | | To follow this tutorial you should be familiar with '''Chimera ''' | + | | | To follow this tutorial, you should be familiar with '''Chimera '''interface. If not, for relevant tutorials, please visit our '''website'''. |
|- | |- | ||
| |00:30 | | |00:30 | ||
− | | | Here I am using '''Ubuntu''' | + | | | Here, I am using '''Ubuntu OS''' version. '''14.04''' ,'''Chimera''' version '''1.10.2''' , '''Mozilla firefox''' browser '''42.0''' and a working internet connection. |
|- | |- | ||
| | 00:46 | | | 00:46 | ||
− | | | Here I have opened a '''Chimera''' window. | + | | | Here, I have opened a '''Chimera''' window. |
|- | |- | ||
| | 00:49 | | | 00:49 | ||
− | | | Using '''command line''', open a structure of '''Squalene Synthase.''' It is a '''Transferace | + | | | Using '''command line''', open a structure of '''Squalene Synthase.''' It is a '''Transferace enzyme''' with a '''pdb code 3w7f'''. |
|- | |- | ||
| | 01:00 | | | 01:00 | ||
− | | |On the '''command line''', | + | | |On the '''command line''', type''' Open space 3w7f'''. Press '''Enter'''. |
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| | 01:12 | | | 01:12 | ||
− | | |Change the display to '''Interactive 1, '''using '''Presets | + | | |Change the display to '''Interactive 1, '''using '''Presets''' menu. |
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| | 01:21 | | | 01:21 | ||
− | | |To delete one of the copies, type '''delete colon dot a''' | + | | |To delete one of the copies, type '''delete colon dot a''', press '''Enter'''. |
|- | |- | ||
| | 01:29 | | | 01:29 | ||
− | | | To delete solvent molecules from the structure, type '''delete solvent'''Press '''Enter'''. | + | | | To delete solvent molecules from the structure, type: '''delete solvent'''. Press '''Enter'''. |
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| | 01:43 | | | 01:43 | ||
− | | | Label the '''ligand residues''' using '''commands'''. Type | + | | | Label the '''ligand residues''' using '''commands'''. Type: '''rlabel '''space''' ligand'''. Press '''Enter'''. |
|- | |- | ||
| | 01:53 | | | 01:53 | ||
− | | | There are two''' farnesyl thiopyrophosphate | + | | | There are two''' farnesyl thiopyrophosphate,''' that is, '''FPS '''for short in this structure. |
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| | 02:08 | | | 02:08 | ||
− | | | There are several side chains that can donate | + | | | There are several side chains that can donate hydrogen bonds to '''phosphate oxygens''' of '''FPS'''. |
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| | 02:23 | | | 02:23 | ||
− | | |Now, | + | | |Now, let's measure the distance between oxygen of '''Serine 21''' and nearest '''phosphate oxygen''' of '''FPS.''' |
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| | 03:20 | | | 03:20 | ||
− | | | '''Hydrogen bonds''' with donor and acceptor distances of 2.2 to 2.5 '''Angstroms''' are classified as strong | + | | | '''Hydrogen bonds''' with '''donor''' and '''acceptor''' distances of 2.2 to 2.5 '''Angstroms''' are classified as strong, 2.5 to 3.2 as moderate, 3.2 to 4.0 as weak. |
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| | 03:40 | | | 03:40 | ||
− | | |Scroll down to residue option, click on '''FPS''' from the sub-menu. | + | | |Scroll down to '''residue''' option, click on '''FPS''' from the sub-menu. |
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| | 03:55 | | | 03:55 | ||
− | | |Click on '''FindHbond''' in the''' Structure Analysis | + | | |Click on '''FindHbond''' in the''' Structure Analysis''' option. |
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| | 04:09 | | | 04:09 | ||
− | | |Fix the line width to 3.0 for a thicker line. | + | | |Fix the '''line width''' to 3.0 for a thicker line. |
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| | 04:26 | | | 04:26 | ||
− | | | And click on '''Write information to reply log'''. | + | | | And, click on '''Write information to reply log'''. |
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| | 04:42 | | | 04:42 | ||
− | | | Details of the bonds can viewed on the '''Reply log'''. | + | | | Details of the bonds can be viewed on the '''Reply log'''. |
|- | |- | ||
| | 04:45 | | | 04:45 | ||
− | | |Open '''Reply log '''using''' Favorites | + | | |Open '''Reply log '''using''' Favorites''' menu. |
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| |04:55 | | |04:55 | ||
− | | | If you want to remove the '''hydrogen bonds''' from the structure | + | | | If you want to remove the '''hydrogen bonds''' from the structure- on the command line, type: The Tilda symbol followed by '''hbond'''. Press '''Enter'''. |
|- | |- | ||
| |05:07 | | |05:07 | ||
− | | | There is another feature in the''' Tools''' menu under '''Structure Analysis''' option. | + | | | There is another feature in the''' Tools''' menu, under '''Structure Analysis''' option. |
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| | 05:26 | | | 05:26 | ||
− | | | | + | | | '''Clashes''' are unfavorable interactions where atoms are too close together. |
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| | 05:33 | | | 05:33 | ||
− | | | | + | | |'''Contacts''' are all direct interactions, polar and non-polar, favorable and unfavorable (including clashes). |
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| | 05:52 | | | 05:52 | ||
− | | |Click on '''Designate''' in the '''Find Clashes/Contacts | + | | |Click on '''Designate''' in the '''Find Clashes/Contacts''' dialog box. |
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| | 06:11 | | | 06:11 | ||
− | | | Under '''Treatment of Clash/Contact Atoms,''' click on the following check boxes. '''Select''' '''Draw pseudo-bonds''' | + | | | Under '''Treatment of Clash/Contact Atoms,''' click on the following check boxes. '''Select''', '''Draw pseudo-bonds''', '''If endpoint atom hidden''', and '''Write information to reply log'''. |
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| | 06:54 | | | 06:54 | ||
− | | | On the '''command line''' type: '''focus space colon 248''' Press '''Enter'''. | + | | | On the '''command line''', type: '''focus space colon 248'''. Press '''Enter'''. |
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| | 07:15 | | | 07:15 | ||
− | | |Press up arrow key on the | + | | |Press up-arrow key on the keyboard to select the entire molecule. |
|- | |- | ||
| | 07:20 | | | 07:20 | ||
− | | | Now we will rotate the side-chain '''Tyrosine 248''' interactively and check for '''Clashes'''. | + | | | Now, we will rotate the side-chain '''Tyrosine 248''' interactively and check for '''Clashes'''. |
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| | 07:32 | | | 07:32 | ||
− | | |On the '''command line''' type display, '''disp space colon 248 space z less than four. ''' (disp :248 z<4) Press '''Enter'''. | + | | |On the '''command line''', type: display, '''disp space colon 248 space z less than four. ''' (disp :248 z<4) Press '''Enter'''. |
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| | 07:59 | | | 07:59 | ||
− | | | Set the '''Clash/Contact Parameters''' to '''Clash. ''' . The ''' Treatment of Clash/Contact Atoms''' to '''Select''' | + | | | Set the '''Clash/Contact Parameters''' to '''Clash. ''' . The ''' Treatment of Clash/Contact Atoms''' to '''Select''', '''Draw pseudobonds''', '''If end point atom hidden'''. |
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| | 08:18 | | | 08:18 | ||
− | | | To rotate the side-chain of '''Tyrosine 248''' interactively | + | | | To rotate the side-chain of '''Tyrosine 248''' interactively- |
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| | 08:22 | | | 08:22 | ||
− | | | | + | | |while pressing '''CTRL''' key, double-click on the '''bond''' that is attached to the '''ribbon'''. |
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| | 08:55 | | | 08:55 | ||
− | | | To revert bond back to the original position: | + | | | To revert bond back to the original position: click the entry under '''Bond'''. Choose '''Revert'''. |
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| | 10:06 | | | 10:06 | ||
− | | | Now to add Hydrogen bonds: | + | | | Now, to add Hydrogen bonds: click on '''Columns''', scroll down to '''Add''', and select '''hydrogen bonds.''' |
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| | 10:35 | | | 10:35 | ||
− | | | Let's summarize. In this tutorial we have learnt to- | + | | | Let's summarize. In this tutorial, we have learnt to- measure distance between atoms in the structure, |
|- | |- | ||
| | 10:43 | | | 10:43 | ||
− | | | | + | | |show '''Hydrogen bonds''', identify non-polar interactions, |
|- | |- | ||
| | 10:48 | | | 10:48 | ||
− | | | | + | | |rotate bonds in the residues to find '''clashes''' and '''contacts''' and compare different '''rotamers'''. |
|- | |- | ||
| |10:56 | | |10:56 | ||
− | | | For the assignment | + | | | For the assignment- open a structure of '''Squalene Synthase''', '''pdb code 3w7f .''' |
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| | 11:11 | | | 11:11 | ||
− | | | The video at the following link summarizes the '''Spoken Tutorial | + | | | The video at the following link summarizes the '''Spoken Tutorial''' project. Please download and watch it. |
|- | |- | ||
| |11:17 | | |11:17 | ||
− | | | The '''Spoken Tutorial | + | | | The '''Spoken Tutorial''' project team conducts workshops and gives certificates for those who pass an on line test. For more details, please write to us. |
|- | |- | ||
| |11:27 | | |11:27 | ||
− | | | | + | | | Spoken Tutorial project is funded by''' NMEICT, MHRD''', Government of India. More information on this mission is available at the '''link''' shown. |
|- | |- | ||
| | 11:37 | | | 11:37 | ||
− | | | This is | + | | | This is Snehalatha from IIT Bombay, signing off. Thank you for joining. |
|} | |} |
Latest revision as of 14:58, 28 June 2018
Time | Narration |
00:01 | Welcome to this tutorial on Structure Analysis. |
00:05 | In this tutorial, we will learn to : measure distance between atoms in the structure, show Hydrogen bonds, identify non-polar interactions, |
00:16 | and rotate bonds in the residues to get different rotamers. |
00:21 | To follow this tutorial, you should be familiar with Chimera interface. If not, for relevant tutorials, please visit our website. |
00:30 | Here, I am using Ubuntu OS version. 14.04 ,Chimera version 1.10.2 , Mozilla firefox browser 42.0 and a working internet connection. |
00:46 | Here, I have opened a Chimera window. |
00:49 | Using command line, open a structure of Squalene Synthase. It is a Transferace enzyme with a pdb code 3w7f. |
01:00 | On the command line, type Open space 3w7f. Press Enter. |
01:09 | A model of the enzyme is displayed on the panel. |
01:12 | Change the display to Interactive 1, using Presets menu. |
01:18 | The protein is displayed as two copies. |
01:21 | To delete one of the copies, type delete colon dot a, press Enter. |
01:29 | To delete solvent molecules from the structure, type: delete solvent. Press Enter. |
01:37 | In this structure, the ligand is farnesyl thiopyrophosphate. |
01:43 | Label the ligand residues using commands. Type: rlabel space ligand. Press Enter. |
01:53 | There are two farnesyl thiopyrophosphate, that is, FPS for short in this structure. |
02:01 | The structures are shown in sticks display. |
02:05 | Rotate the structure and zoom-in. |
02:08 | There are several side chains that can donate hydrogen bonds to phosphate oxygens of FPS. |
02:15 | Place the cursor over the atoms in the side-chain residues. |
02:21 | Locate Serine 21 residue. |
02:23 | Now, let's measure the distance between oxygen of Serine 21 and nearest phosphate oxygen of FPS. |
02:32 | To measure the distance, select oxygen of Serine 21 residue. |
02:37 | While pressing the CTRL key, click on the side chain oxygen of Serine 21. |
02:43 | While pressing CTRL and Shift keys simultaneously, double-click on the nearest phosphate oxygen of FPS. |
02:52 | Select Show Distance from the context menu. |
02:56 | Observe the panel. The distance between two atoms is displayed. Clear selection. |
03:04 | Similarly, measure distance between side-chain oxygen of Tyrosine and the same phosphate oxygen of FPS. |
03:15 | The distances seem consistent with hydrogen bonds. |
03:20 | Hydrogen bonds with donor and acceptor distances of 2.2 to 2.5 Angstroms are classified as strong, 2.5 to 3.2 as moderate, 3.2 to 4.0 as weak. |
03:36 | Now, select the ligand using Select menu. |
03:40 | Scroll down to residue option, click on FPS from the sub-menu. |
03:46 | The easy way to find hydrogen bonds formed by FPS is to use Find Hydrogen bond feature from Tools menu. |
03:55 | Click on FindHbond in the Structure Analysis option. |
04:01 | A H-Bond Parameters dialog opens. |
04:05 | Fix the color of the hydrogen bond by clicking on the colored box. |
04:09 | Fix the line width to 3.0 for a thicker line. |
04:13 | Click on the check box against Label Hydrogen bond with distance. |
04:21 | Click on Only find H-bonds with at least one end selected. |
04:26 | And, click on Write information to reply log. |
04:31 | Click on OK button. |
04:33 | Observe the panel. Hydrogen bonds are shown as pseudo-bonds of specified color and line width. |
04:42 | Details of the bonds can be viewed on the Reply log. |
04:45 | Open Reply log using Favorites menu. |
04:49 | Information about each hydrogen bond is given here. |
04:53 | Close the dialog box. |
04:55 | If you want to remove the hydrogen bonds from the structure- on the command line, type: The Tilda symbol followed by hbond. Press Enter. |
05:07 | There is another feature in the Tools menu, under Structure Analysis option. |
05:13 | It is Findclashes/contacts. A dialog box opens. |
05:19 | This feature identifies non-polar interactions such as Clashes and Contacts. |
05:26 | Clashes are unfavorable interactions where atoms are too close together. |
05:33 | Contacts are all direct interactions, polar and non-polar, favorable and unfavorable (including clashes). |
05:43 | Let us identify contacts of the FPS residues with all other atoms. |
05:48 | Select FPS residue using Select menu. |
05:52 | Click on Designate in the Find Clashes/Contacts dialog box. |
05:58 | It shows 48 atoms designated. |
06:02 | Click on the radio button against “All other atoms”. |
06:06 | Set the Clash/Contact Parameters to default Contact. |
06:11 | Under Treatment of Clash/Contact Atoms, click on the following check boxes. Select, Draw pseudo-bonds, If endpoint atom hidden, and Write information to reply log. |
06:27 | Click on OK button. Observe the panel. |
06:32 | All the contacts of FPS residues are shown. |
06:37 | Open the Reply Log. . Atom-atom contacts are listed here. |
06:44 | Close the dialog box. |
06:46 | Now let's display some clashes. |
06:49 | Let us focus on the residue Tyrosine 248. |
06:54 | On the command line, type: focus space colon 248. Press Enter. |
07:03 | Clear the selection. |
07:06 | Now select Tyrosine 248 residue. |
07:10 | While pressing the CTRL key, click on any atom in Tyrosine 248. |
07:15 | Press up-arrow key on the keyboard to select the entire molecule. |
07:20 | Now, we will rotate the side-chain Tyrosine 248 interactively and check for Clashes. |
07:27 | Display residues within 4 Angstroms of Tyrosine 248. |
07:32 | On the command line, type: display, disp space colon 248 space z less than four. (disp :248 z<4) Press Enter. |
07:45 | To display the clashes, select FindClashes/Contacts option from the Tools menu. |
07:53 | click on Designate. |
07:55 | Click the button against “All other atoms”. |
07:59 | Set the Clash/Contact Parameters to Clash. . The Treatment of Clash/Contact Atoms to Select, Draw pseudobonds, If end point atom hidden. |
08:11 | And set the Frequency of Checking to Continuously. |
08:15 | Hide the dialog box. |
08:18 | To rotate the side-chain of Tyrosine 248 interactively- |
08:22 | while pressing CTRL key, double-click on the bond that is attached to the ribbon. |
08:29 | Choose rotate bond option from the context menu. |
08:33 | A Build structure dialog opens. |
08:36 | Rotate the bond by dragging the pointer on the dial. |
08:41 | Alternatively, click on the black arrowheads to edit the angle values. |
08:47 | Observe the panel. As the side-chain moves, new pseudo-bonds are formed or disappear. |
08:55 | To revert bond back to the original position: click the entry under Bond. Choose Revert. |
09:03 | Again click on the bond then Deactivate to make the bond no longer rotate-able. |
09:09 | Close the dialog box. |
09:11 | We can compare all the rotamers of Tyrosine 248 using the option in the Tools menu. |
09:18 | First select Tryrosine 248. |
09:22 | Click on Tools menu, scroll down to Structure editing. |
09:26 | Click on Rotamers option. |
09:29 | In the Rotamer dialog box, select Dunbrack from the rotamer library. |
09:36 | Click on OK button. |
09:38 | The rotamers are shown as wire representation on the panel. |
09:43 | Another dialog opens. Click on the lines in the dialog box to display the rotamer. Observe the panel. |
09:52 | We can also detect Clash and hydrogen bonds for the rotamers. |
09:58 | Click on Columns ,then Add. Select Clashes. |
10:03 | Click on OK in the dialog box. |
10:06 | Now, to add Hydrogen bonds: click on Columns, scroll down to Add, and select hydrogen bonds. |
10:15 | Click on OK in the Hydrogen bonds dialog box. |
10:19 | Observe the dialog, two new columns are added. |
10:24 | Now each rotamer forms several Clashes but no hydrogen bonds. |
10:30 | Try finding rotamers by rotating bonds in a different residue. |
10:35 | Let's summarize. In this tutorial, we have learnt to- measure distance between atoms in the structure, |
10:43 | show Hydrogen bonds, identify non-polar interactions, |
10:48 | rotate bonds in the residues to find clashes and contacts and compare different rotamers. |
10:56 | For the assignment- open a structure of Squalene Synthase, pdb code 3w7f . |
11:03 | Rotate bonds in Tyrosine 41, residue to determine Clashes and Contacts. And compare the rotamers. |
11:11 | The video at the following link summarizes the Spoken Tutorial project. Please download and watch it. |
11:17 | The Spoken Tutorial project team conducts workshops and gives certificates for those who pass an on line test. For more details, please write to us. |
11:27 | Spoken Tutorial project is funded by NMEICT, MHRD, Government of India. More information on this mission is available at the link shown. |
11:37 | This is Snehalatha from IIT Bombay, signing off. Thank you for joining. |