Difference between revisions of "UCSF-Chimera/C3/Structure-Analysis/English"

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*On the command line type:  
 
*On the command line type:  
  
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'''The Tilda symbol '''followed by''' hbond '''
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:'''The Tilda symbol '''followed by''' hbond '''
  
  
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'''Clashes and Contacts'''
 
'''Clashes and Contacts'''
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| *'''''Clashes''''' are unfavorable interactions where atoms are too close together.
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"|  
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*'''''Clashes''''' are unfavorable interactions where atoms are too close together.
  
 
*'''''Contacts''''' are all direct interactions: polar and non-polar, favorable and unfavorable (including clashes)  
 
*'''''Contacts''''' are all direct interactions: polar and non-polar, favorable and unfavorable (including clashes)  

Latest revision as of 15:59, 1 July 2016

Visual Cue
Narration
Slide Number 1

Title Slide

Welcome to this tutorial on Structure Analysis.
Slide Number 2

Learning Objectives

In this tutorial, we will learn to,


  • Measure distance between atoms in the structure
  • Show Hydrogen bonds
  • Identify non-polar interactions
  • And rotate bonds in the residues to get different rotamers
Slide Number 3

Pre-requisites

To follow this tutorial you should be familiar with Chimera Interface.

If not, for relevant tutorials, please visit our website.

Slide Number 4

System Requirement

Here I am using
  • Ubuntu OS version. 14.04
  • Chimera version 1.10.2
  • Mozilla firefox browser 42.0
  • And a working Internet connection.
Double-click on the Chimera icon on the desktop. Here I have opened a Chimera window.
Open Command line using Favorites menu.

Type

Open 3w7f

Using command line, open a structure of Squalene Synthase.


It is a Transferace enzyme with a pdb code 3w7f.

On the command line, type

Open space 3w7f

Press Enter.

Open Presets menu, scroll down and click on Interactive1. A model of the enzyme is displayed on the panel.


Change the display to Interactive 1, using Presets menu.

Type

delete:.a

Press enter

The protein is displayed as two copies.

To delete one of the copies, type

delete colon dot a


Press Enter.

Type


delete solvent


Press enter

To delete solvent molecules from the structure, type

delete solvent


Press Enter.

Cursor on the ligand. In this structure, the ligand is farnesyl thiopyrophosphate.


Type

rlabel ligand

press enter

Label the ligand residues using commands.

Type,

rlabel space ligand

Press Enter.

Cursor on the panel There are two farnesyl thiopyrophosphate:

that is, FPS for short in this structure.


The structures are shown in sticks display.

Drag the mouse to rotate.

Scroll the center mouse wheel to zoom.

Rotate the structure and zoom-in.
Cursor on the structure.


Hover the cursor on the structure.

There are several side chains that can donate hydrogen bonds to phosphate oxygens of FPS.


Place the cursor over the atoms in the side-chain residues.

Hover the cursor on the structure. Locate Serine 21 residue.


Now, lets measure the distance between

  • oxygen of Serine 21:
  • and nearest phosphate oxygen of FPS.
Cursor on the structure.


To measure the distance, select oxygen of Serine 21 residue.
While Pressing the CTRL key, click on the side chain oxygen of Serine 21. While pressing the CTRL key, click on the side chain oxygen of Serine 21.
While pressing CTRL and Shift keys simultaneously;

double-click on the nearest phosphate oxygen.

  • While pressing CTRL and Shift keys simultaneously,
  • double-click on the nearest phosphate oxygen of FPS.
Click Show Distance in the resulting context menu. Select Show Distance from the context menu.
Cursor on the panel. Observe the panel.

The distance between two atoms is displayed.


Clear selection.

While pressing CTRL and Shift keys simultaneously;

double-click on oxygen of Tyrosine 248

Similarly, measure distance between
  • side-chain oxygen of Tyrosine
  • and the same phosphate oxygen of FPS.
Cursor on the panel. The distances seem consistent with hydrogen bonds.
Slide Number 5

Hydrogen Bond Distances

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.
Click on Select menu, click on Residue, then FPS. Now, select the ligand using Select menu.


Scroll down to residue option, click on FPS from the sub-menu.

Scroll down the Tools menu >> Structure Analysis >> FindHbond.
  • The easy way to find hydrogen bonds formed by FPS is
  • to use Find Hydrogen bond feature from Tools menu.


Click on FindHbond in the Structure Analysis option.

H-Bond Parameters dialog opens. A H-Bond Parameters dialog opens.


Fix the color of the hydrogen bond by clicking on the colored box.

Fix the line width to 3.0 for a thicker line.

Click on: Label H-bond with distance.


Click on: Only find H-bonds with at least one end selected.


Click ON: Write information to reply log.

  • Click on the check box against Label Hydrogen bond with distance.
  • Click on Only find H-bonds with at least one end selected.
  • And click on Write information to reply log.
Click on OK button. Click on OK button.
Cursor on hydrogen bond.


Zoom the model.

Observe the panel.


Hydrogen bonds are shown as pseudo-bonds of specified color and line width.

Click on Favorites >> Reply log. Details of the bonds can viewed on the Reply log.


Open Reply log using Favorites menu.


A Reply log dialog box opens.


Close the dialog box.

Information about each hydrogen bond is given here.


Close the dialog box.

Type,

~hbond


Press enter

  • If you want to remove the hydrogen bonds from the structure,
  • On the command line type:
The Tilda symbol followed by hbond


Press Enter.

Click on Tools menu >> Findclashes/contacts. There is another feature in the Tools menu under Structure Analysis option.


It is Findclashes/contacts.


A dialog box opens.


This feature identifies non-polar interactions such as Clashes and Contacts.

Slide Number 6

Clashes and Contacts

  • Clashes are unfavorable interactions where atoms are too close together.
  • Contacts are all direct interactions: polar and non-polar, favorable and unfavorable (including clashes)
Cursor on the panel.


Click on Select menu.

Choose FPS from Residue sub-menu.


Click on Designate in the Find Clashes/Contacts dialog box.

Let us identify contacts of the FPS residues with all other atoms.


Select FPS residue using Select menu.


Click on Designate in the Find Clashes/Contacts dialog box.

Point to the number. It shows 48 atoms designated.
Click the radio button against “all other atoms”. Click on the radio button against “All other atoms”.
Set the Clash/Contact Parameters to the default Contact.

Click on contact button.

Set the Clash/Contact Parameters to default Contact.
Set the Treatment of Clash/Contact Atoms to:


Click on

Select

Draw pseudo-bonds

If endpoint atom hidden, show endpoint residue

Write information to reply log


Turn off any other Treatment option.

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
Click on Apply option. Click on OK button.


Observe the panel.


All the contacts of FPS residues are shown.

Favorites menu >> Reply Log.


Open the Reply Log.


Atom-atom contacts are listed here.

Cursor on Reply log. Close the dialog box.
Cursor on the panel. Now let's display some clashes.


Let us focus on the residue Tyrosine 248.

On the command line type :


focus :248

Press enter.

On the command line type:

focus space colon 248

Press Enter.

Press CTRL key and click on the panel. Clear the selection.
While pressing the CTRL key click on any atom or bond in Tyr 248.


Press up arrow key on the keyboard.

Now select Tyrosine 248 residue.


While pressing the CTRL key, click on any atom in Tyrosine 248.


Press up arrow key on the keyboard to select the entire molecule.

Cursor on the panel. Now we will rotate the side-chain Tyrosine 248 interactively and check for Clashes.
On the command line type

disp :248 z<4


Press Enter.

Display residues within 4 Angstroms of Tyrosine 248.


On the command line type display,


disp space colon 248 space z less than four.


(disp :248 z<4)


Press Enter.

Select Fine Clashes/Contacts option from the Tools menu. To display the clashes, select FindClashes/Contacts option from the Tools menu.
In the Find Clashes dialog box, click on Designate. In the dialog box, click on Designate.


Click the button against “All other atoms”.

Click on Clash button.

Set the Treatment of Clash/Contact Atoms to Draw pseudobonds.


Set the Frequency of Checking to Continuously.

Set the Clash/Contact Parameters to Clash.


The Treatment of Clash/Contact Atoms to

  • Select
  • Draw pseudobonds
  • If end point atom hidden
  • And set the Frequency of Checking to Continuously.
Click on minimize button. Hide the dialog box.
While pressing ctrl key, double-click on the bond that is attached to the ribbon.


Choose rotate bond from the context menu.

To rotate the side-chain of Tyrosine 248 interactively;


While pressing CTRL key, double-click on the bond that is attached to the ribbon.


Choose rotate bond option from the context menu.

Rotate the bond by dragging the pointer on the dial.


Click on the black arrowheads to edit the angle values.

A Build structure dialog opens.


Rotate the bond by dragging the pointer on the dial.


Alternatively, click on the black arrowheads to edit the angle values.

Cursor on Find clashes dialog box.


Drag the pointer.

Observe the panel.


As the side-chain moves, new pseudo-bonds are formed or disappear.


Click the entry under Bond to show a menu.


Choose Revert.

To revert bond back to the original position:
  • Click the entry under Bond.
  • Choose Revert.
  • Again click on the bond then Deactivate to make the bond no longer rotate-able.
Close the dialog. Close the dialog box.
Select Try 248.


Click on Tools menu, then Structure editing, select Rotamers from the sub-menu.


In the rotamer dialog box, select Dunbrack from the rotamer library.

We can compare all the rotamers of Tyrosine 248 using the option in the Tools menu.
  • First select Tryrosine 248.
  • Click on Tools menu, scroll down to Structure editing.
  • Click on Rotamers option.
  • In the Rotamer dialog box, select Dunbrack from the rotamer library.
Click OK button.


Cursor on the panel.

Click on OK button.


The rotamers are shown as wire representation on the panel.

Click on the line in the dialog. Another dialog opens.

Click on the lines in the dialog box to display the rotamer.


Observe the panel.

Cursor on the panel. We can also detect Clash and hydrogen bonds for the rotamers.
Click on Columns >> Add>> Clashes>> Click on OK Click on Columns ,then Add.

Select Clashes.

Click on OK in the dialog box.

Click on Columns >> Add>> Clashes>> Click on OK. Now to add Hydrogen bonds:

Click on Columns, scroll down to Add, and select hydrogen bonds.

Click on OK in the Hydrogen bonds dialog box.

Click on the dialog. Observe the dialog, two new columns are added.

Now each rotamer forms several Clashes but no hydrogen bonds.

Try finding rotamers by rotating bonds in a different residue.

Slide Number 7

Summary

Let's summarize.

In this tutorial we have learnt to-

  • Measure distance between atoms in the structure
  • Show Hydrogen bonds
  • Identify non-polar interactions
  • Rotate bonds in the residues to find clashes and contacts.
  • And compare different rotamers.
Slide Number 8

Assignment

For the assignment,
  • Open a structure of Squalene Synthase, pdb code 3w7f .
  • Rotate bonds in Tyrosine 41, residue to determine Clashes and Contacts.
  • And compare the rotamers.
Slide Number 9

Acknowledgement

The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

Slide Number 10 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.

Slide number 11 Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this Mission is available at the link shown

This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Nancyvarkey, Snehalathak

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