Difference between revisions of "UCSF-Chimera/C2/Picking-and-Selection/English"

Title Slide

Learning Objectives

• Show labels for atoms and residues.
• Select atoms and residues using Select menu or by Picking.
• Change the color and display of the residues.
• Add, delete or change atoms
• Rotate bonds

Learning Objectives

• Select and move the model.

Pre-requisites

Undergraduate Biochemistry.

Or familiar with structural biology.

For relevant tutorials, please visit our website.

http://spoken-tutorial.org

System Requirement

Ubuntu Operating System version. 14.04

Chimera version 1.10.2

Mozilla firefox browser 35.0

And a working internet connection.

Click on “1zik' on the rapid access window.

On the rapid access window, click on 1zik from the list of recently accessed data.

A model of Leucine zipper opens on the graphics window.

residues, atoms, bonds etc can be modified using tools available in Chimera.

The first step is to make selection.

Ways to make a Selection

• using the Select menu in the menu bar.
  

• Picking from the graphics window.
  

• Typing commands on the command line.
• Or by selecting, Model Panel and Sequence option present in the Favorites menu.

Leucine zipper motif consists of periodic repetition of leucine residues.

I will now demonstrate how to highlight the leucine residues present in this structure.

Click on interactive 2.

Scroll down the Select menu.

This will convert the structure to atoms display.

From the Select menu choose Residue option.

The sub-menu has many options.

aliphatic, aromatic, hydrophobic, polar etc.

Click on leucine.

Click on leucine.

All the leucine residues are now highlighted.

Cursor on the structure.

I will choose yellow from the list of colors.

All the leucines are now displayed in yellow color.

Click on Clear selection option.

Then click on Clear selection option.

Click on Interactive 1.

Click on Interactive 1.

Hover the cursor over the structure.

Hover the cursor over the structure.

It has information such as residue name, residue number and Chain.

Release the CTRL key.

By default the selection is outlined in green.

Click on the residues.

Press and hold both CTRL and shift key on the key board.

Hover the mouse over the peptide chain.

Click on the residues you want to pick.

Release the CTRL and Shift keys from the key board.

Scroll down and click on atoms/bonds.

Click on “show”.

Click on Actions menu.

For example to display atoms, choose atoms/bonds.

Click on Show.

Clear the selection.

This will show its label information in an atomspec balloon.

Residue name, number, chain and atom name.

Scroll down the context-menu.

While holding the CTRL key click on the atom you want to change.

Double-click on the atom while holding the CTRL key.

To modify the atom double-click on the atom while holding the CTRL key.

Click on Modify-atom option.

Release the CTRL key.

Click on Modify-atom option.

Release the CTRL key.

Let us change the selected atom that is Nitrogen to a methyl group.

Click on apply button.

Observe the panel.

A methyl group is now added to the existing structure.

Close the window.

Cursor on the pop-up balloon.

Hover the cursor over the bond you want to rotate.

Information regarding the bond appears in the atomspec balloon.

Press and hold the CTRL key.

Click the left mouse button.

While still pressing the CTRL key double click on the bond.

While still holding the CTRL key double click on the bond.

Release the CTRL key on the key board.

Click on rotate bond option.

A Build Structure dialog box appears on the screen.

Observe the panel. The selected bond is now rotating.

Stop rotating when you reach the desired angle.

Close the dialog box.

Scroll down the tools menu and click on Sequence option.

Choose Sequence from the sub-menu.

Click on chain A, then click on show button.

Cursor on the dialog box.

Click on chain A if you want to select chain A.

Then click on show.

Another dialog box appears on screen with the amino acid sequence.

Click on the sequence to select.

Click on quit to close the window.

Click on yellow.

Click on yellow option.

Chain A is now in yellow color.

Clear the selection.

“Fetch structure window”, select PDB option.

Scroll down the file menu.

Click on Fetch by ID.

A Fetch structure by ID dialog box opens.

Select PDB option.

Click on fetch button.

For example to fetch human insulin, type 4ex1.

Click on fetch button.

We have to selectively move one model on the panel.

Scroll down and click on Command line option.

On command line, Click on the small square box for zero.

The Command line appears at the bottom of the window.

Click to uncheck model zero, which represents leucine zipper.

Hold the center mouse button.

Drag to move the insulin model to the desired location on the panel.

Release the mouse button.

Clicking on the model ID.

Open the model panel using Favorites menu.

A Model Panel dialog box appears.

For example I want to remove the insulin model from the screen.

Click on close option.

Click on close option.

The model of insulin is now removed from the screen.

Close the model panel window.

Summary

Summary

• Show labels for atoms and residues.
• Select atoms and residues using Select menu or by Picking.
• Change the color and display of the residues.
• Add, delete or change atoms
• Rotate bonds

Summary

• Select and move the model.

Assignment

Open a structure of human insulin, pdb code 4ex1 on the Chimera window.

Color all the hydrophobic amino acid residues in blue.

Color all polar residues in red.

Your completed assignment should look as follows.

Acknowledgement

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Acknowledgement

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Acknowledgement

More information on this Mission is available at the link shown

Acknowledgement