Week 5 - Introduction to UCSF Chimera

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.

First go to https://www.cgl.ucsf.edu/chimera/download.html and download the appropriate software for your operating system.

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Rotating and magnifying a protein

Example 1: View “crystal structure of quinine reductase II” (PDB ID: 2QX4)

1. Create a folder named pdb files on your Desktop.
2. Download the PDB file of 2QX4 into the folder you created.
3. Open the structure:
4. Menu bar: File → Open → select 2QX4.pdb, or
5. Fetch from internet: File → Fetch by ID → check PDB → enter 2QX4
6. Manipulate the structure:
7. Click and drag to rotate.
8. Scroll forward to zoom out; backward to zoom in.
9. Click and drag with the mouse wheel pressed to reposition the protein.

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Visualization styles of proteins in UCSF Chimera

Example 2: Display 2QX4 in different styles

1. From the menu bar:
2. Actions → Atoms/Bonds → show
3. Actions → Ribbon → hide
4. Try different atom/bond styles:
5. Actions → Atoms/Bonds → wire
6. Actions → Atoms/Bonds → stick
7. Actions → Atoms/Bonds → ball and stick
8. Actions → Atoms/Bonds → sphere
9. Display the protein in stick form, then:
10. Actions → Ribbon → show
11. Observe side chains on the ribbon.
12. Change ribbon style:
13. Actions → Ribbon → flat / edged / round
14. To return to original state:
15. Presets → Interactive 1 (ribbons)

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Selecting

Example 3

1. Select chains:
2. Select → Chain → A
3. Select → Chain → B
4. Before selecting residues/elements:
5. Display atoms as sticks and hide ribbons (as in Example 2).
6. Selection examples:
7. Select → Chemistry → element → N (nitrogen)
8. Select → Chemistry → functional group → carboxylate
9. Select → Residue → amino acid category → aromatic
10. Select → Residue → FAD
11. Select → Residue → GLN
12. Select → Structure → ligand
13. Clear selection:
14. Select → Clear Selection, or
15. Press Ctrl and click an empty point on the screen.

Keyboard/interaction shortcuts:

• Press Ctrl and click an atom to select.
• Press ↑ once to expand selection to the residue.
• Press ↑ again to expand selection to the chain.
• Undo these expansions using ↓.

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Coloring

Example 4

1. Go to Presets → Interactive 1 (ribbons).
2. This will show two chains in blue and red.
3. Select arginine residues (as in Example 3) and color them:
4. Actions → Color → Yellow
5. Select histidine residues and color them:
6. Actions → Color → Cyan
7. Color α-helices purple:
8. Select → Structure → Secondary Structure → Helix
9. Actions → Color → Purple
10. Go to ball and stick style and color the protein forest green.
11. To return to original element-based colors:
12. Actions → Color → by element

Background color:

1. Actions → Color → check background

1. Actions → Color → Gray (or any other color)

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Surface

Example 5

1. Actions → Surface → show
2. This displays the solid molecular surface.
3. Other surface styles:
4. Actions → Surface → mesh
5. Actions → Surface → dot
6. After exploring, return to solid surface mode.
7. Select ligands and display a mesh surface around them.
8. Change surface color:
9. Actions → Color → Magenta
10. Select ligands and display a solid surface around them, then color those surfaces blue.
11. Hide surfaces:
12. Actions → Surface → hide

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Labeling

Example 6: Label atoms on FAD

1. Select → Residue → FAD
2. Actions → Atoms/Bonds → show only
3. Actions → Label → element (or name)
4. Select and display chain A only:
5. Select → Chain → A
6. Label residues:
7. Actions → Label → residue → name (or 1-letter code)
8. Turn off labels:
9. Actions → Label → residue → off

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Deleting atoms/residues

Example 7

1. View the protein in ball and stick format.
2. Select an amino acid residue.
3. Actions → Atoms/Bonds → delete
4. Select chain B and delete it.

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Tools

Depiction

Example 8

1. Close the previous session:
2. File → Close Session
3. Re-open the structure.
4. Try:
5. Tools → Depiction → Color Secondary Structure
6. Tools → Depiction → Rainbow
7. Tools → Depiction → Pipes and Planks
8. Then hide ribbons:
9. Actions → Ribbon → hide

Structure Analysis

Example 9

Displaying H-bonds:

1. Display the structure in stick style.
2. Tools → Structure Analysis → FindHBond

Measuring distances:

1. Select atom 1: Ctrl + Left Click
2. Select atom 2: Ctrl + Shift + Left Click
3. Tools → Structure Analysis → Distances → Create

Measuring angles/torsions:

• Select three atoms similarly → Tools → Structure Analysis → Angles/Torsions → Create
• Select four atoms similarly → Tools → Structure Analysis → Angles/Torsions → Create

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Structure Comparison

Example 10

MatchMaker

1. Open:
2. 1tag transducin bound to Gα-GDP
3. 1tnd transducin bound to Gα-GTP γS
4. Tools → Structure Comparison → MatchMaker
5. Select:
6. reference structure: 1tag
7. structure(s) to match: select both
8. Click Apply.

To analyze the chimeric structure better, delete chain B and C of 1tnd:

1. Select → Chain → B → Actions → Atoms/Bonds → delete
2. Select → Chain → C → Actions → Atoms/Bonds → delete

Compare and contrast the chimeric regions on the two proteins and comment on why some regions differ.

Morph Conformations

1. Tools → Morph Conformations → Add
2. Add both 1tag and 1tnd → Create

A movie window will pop up showing the transition between conformations.

Tile Structures

• Tools → Structure Comparison → Tile Structures

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Sequence

Example 11: Display sequence of 1tag

1. Tools → Sequence → Sequence
2. Select 1tag → click Show

Notes:

• Yellow highlights correspond to helices.
• Green highlights correspond to strands.
• Select a region by left click + drag.

Match → Align

1. Open 3EML (adenosine A2A receptor) and 3NY8 (β2-adrenergic receptor).
2. Create a matched/chimeric structure using MatchMaker.
3. Tools → Sequence → Match → Align → select both → Apply.
4. Interpret the alignment.

Blast Protein

• Tools → Sequence → Blast Protein → select 3EML → Apply

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Structure Editing

Example 12: Edit 1TAG

Open 1TAG and display it in sticks style.

Adding hydrogens:

• Tools → Structure Editing → AddH

You can display hydrogen bonds as well:

• Tools → Structure Binding Analysis → FindHBond

Adjust torsions:

1. Close the previous session and re-open 1tag.
2. Select exactly one bond by Ctrl + Left click + drag.
3. Tools → Structure Editing → Adjust Torsions

Build structure:

1. Tools → Structure Editing → Build Structure → Modify atom
2. Set:
3. Element: N
4. Bonds: 3

1. Select a carbon atom from the structure.
2. Return to the Build Structure window and click Change.
3. To delete bonds:
4. Select a bond
5. Tools → Structure Editing → Build Structure → Add/Delete Bonds → click Delete selected bonds

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Higher-Order Structure

Example 13: Multiscale models

Open 1K4C (potassium channel).

1. Tools → Higher-Order Structure → Multiscale Models
2. Click Make Models at the bottom of the window.
3. You will see the tetrameric form of the potassium channel; new subunits appear as surfaces.
4. Select all surfaces and add ribbons to them, then hide surfaces.