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

Title Slide

Learning Objectives

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

Pre-requisites

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System Requirement

• Ubuntu OS version. 14.04
• Chimera version 1.10.2
• Mozilla firefox browser 42.0
• And a working Internet connection.

Type

Open 3w7f

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

On the command line, type

Open space 3w7f

Press Enter.

Change the display to Interactive 1, using Presets menu.

delete:.a

Press enter

To delete one of the copies, type

delete colon dot a

Press Enter.

delete solvent

Press enter

delete solvent

Press Enter.

rlabel ligand

press enter

Type,

rlabel space ligand

Press Enter.

that is, FPS for short in this structure.

The structures are shown in sticks display.

Scroll the center mouse wheel to zoom.

Hover the cursor on the structure.

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

Now, lets measure the distance between

• oxygen of Serine 21:
• and nearest phosphate oxygen of FPS.

double-click on the nearest phosphate oxygen.

• While pressing CTRL and Shift keys simultaneously,
• double-click on the nearest phosphate oxygen of FPS.

The distance between two atoms is displayed.

Clear selection.

double-click on oxygen of Tyrosine 248

• side-chain oxygen of Tyrosine

and the same phosphate oxygen of FPS.

Hydrogen Bond Distances

• 2.2 to 2.5 Angstroms are classified as strong.
• 2.5 to 3.2 as moderate.
• 3.2 to 4.0 as weak.

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

• 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.

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: 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.

Zoom the model.

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

Open Reply log using Favorites menu.

Close the dialog box.

Close the dialog box.

~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.

It is Findclashes/contacts.

A dialog box opens.

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

Clashes and Contacts

• Contacts are all direct interactions: polar and non-polar, favorable and unfavorable (including clashes)

Click on Select menu.

Choose FPS from Residue sub-menu.

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

Select FPS residue using Select menu.

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

Click on contact button.

Click on

Select

Draw pseudo-bonds

If endpoint atom hidden, show endpoint residue

Write information to reply log

Turn off any other Treatment option.

• Select
• Draw pseudo-bonds
• If endpoint atom hidden
• And Write information to reply log

Observe the panel.

All the contacts of FPS residues are shown.

Atom-atom contacts are listed here.

Let us focus on the residue Tyrosine 248.

focus :248

Press enter.

focus space colon 248

Press Enter.

Press up arrow key on the keyboard.

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

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

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.

Click the button against “All other atoms”.

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

Set the Frequency of Checking to Continuously.

The Treatment of Clash/Contact Atoms to

• Select
• Draw pseudobonds
• If end point atom hidden
• And set the Frequency of Checking to Continuously.

Choose rotate bond from the context menu.

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

Choose rotate bond option from the context menu.

Click on the black arrowheads to edit the angle values.

Rotate the bond by dragging the pointer on the dial.

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

Drag the pointer.

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

Choose Revert.

• Click the entry under Bond.
• Choose Revert.
• Again click on the bond then Deactivate to make the bond no longer rotate-able.

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

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

• 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.

Cursor on the panel.

The rotamers are shown as wire representation on the panel.

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

Observe the panel.

Select Clashes.

Click on OK in the dialog box.

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

Click on OK in the Hydrogen bonds dialog box.

Now each rotamer forms several Clashes but no hydrogen bonds.

Try finding rotamers by rotating bonds in a different residue.

Summary

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.

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.

Acknowledgement

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