Week 6 - UCSF Chimera Tutorials

1. Molecular Bracelet - Creating an image with per-model clipping

1. Open the molecule with PDB ID: 1rf8.
2. Solution structure of the yeast translation initiation factor eIF4E in complex with m7GDP and eIF4GI residues 393 to 490.
3. Favorites → Command Line
4. In the command line, type:

delete #0.2-11

1. Press Enter.
2. Presets → Interactive 1 (ribbons)
3. In the command line, type:

surfcat partb :.b

1. Press Enter.

The surfcat command tells Chimera to generate a surface that encloses just chain B instead of chains A and B together.

1. In the command line, type:

surf partb

1. Press Enter.
2. Actions → Surface → Transparency → choose a percentage.
3. Tools → Depiction → Per-Model Clipping
4. Actions → Color → check Surfaces
5. Actions → Color → Red
6. Tools → Depiction → Surface Capping → change cap color to Orange
7. Select Chain B
8. Actions → Color → click on the dashed line at the very top
9. Check ribbons from the list and choose yellow as the color
10. Change background color to sky blue
11. Command line:

rock y -4 120

1. Command line:

scale 1.05 20

1. Tools → Utilities → Movie Recorder
2. Click the Browse icon beside Output file
3. Create a file named molecular bracelet on Desktop
4. Click Record and rotate/zoom the molecule as desired
5. Click Stop
6. Click Make movie
7. Play the movie after processing is complete

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2. GroEL visualization (EM density map + atomic model)

1. Download electron microscopy data from EMDB:
2. https://pdbj.org/emnavi/quick.php?id=emdb-1080
3. Type 1080 in the query box.

1. In the new window, click Downloads from the left-hand side.
2. Download the map and continue.
3. Open emd_1080.map (electron microscopy view of GroEL).
4. The Volume Viewer window will pop up automatically.

1. Move the gray bar on the histogram to the left or set Level to 0.950.
2. Click the gray square near Color to change the map color.
3. In the Style section, you can change view style (e.g., mesh).
4. Open 1OEL.pdb (crystal structure of GroEL).
5. Hide the GroEL map:
   • Favorites → Model Panel

1. Uncheck S for emd_1080.map to hide it.
2. Color each chain of 1OEL to a different color.
3. Show emd_1080.map again by checking S.
4. To fit the ribbon model into the density map, deactivate the map by unchecking A for emd_1080.map.
5. Fit the ribbon into the electron density map.
6. Activate the map again and display the surface around it using the Volume Viewer window.
7. Set surface transparency to 20% and save an image:
   • File → Save Image
8. Hide the ribbon and make the surface fully opaque (transparency 0%).
9. Tools → Depiction → Per-Model Clipping → enable clipping
10. Check Adjust clipping with mouse as below
11. Set the area where you want to clip the surface.
12. Tools → Depiction → Surface Capping → check both options to color the cap.

1. Tools → Volume Data → Surface Color
2. Set the coloring options as desired. To set the color range, use Set.

1. (Optional) Close and open only 1OEL.pdb.
2. Tools → Higher-Order Structure → Multi-Scale Models
   • Choose Crystal unit cell as Multimer type (instead of Biological oligomer).

Exercise 1

Make a crystal unit cell oligomer of chaperonin with PDB ID: 1AON.

• Delete all models except one.
• Make the surface 30% transparent.
• Display ribbons inside.
• Clip the long side of the molecule and color the surface cap.

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3. Density maps and large molecular assemblies

1. Open emd_1015.map.
2. You can also Fetch by ID, but check EMDB first (not PDB).
3. Set level to 7000 by moving the histogram bar or typing the value into the Level box.

1. Change color as in Tutorial 2.
2. Cut the surface from the center using Per-Model Clipping.
3. Color the surface by radius:
4. Tools → Volume Data → Surface Color → by radius

1. Click Color.
2. Change the level to 2000 to show the center of the particle.
3. Open 1dyl.pdb1 to view both ribbon and surface map together.

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4. Movie making with maltotriose-bound and unbound conformations

1. Open PDB ID: 2gha.
2. Select chain B and delete it.
3. File → Save PDB → file name: 2gha-chainA
4. Close this session and open 2ghb.
5. Select chain A, then Select → Invert (selected models).
6. Delete them.
7. File → Save PDB → file name: 2ghb-chainA
8. Open both saved files and align them with MatchMaker.
9. Create Morph Conformations.
10. Hide ribbons of 2gha-chainA and 2ghb-chainA, but display MLR.
11. Open command line and type:

show #2 & ligand zr<5

This displays residues within a cutoff distance to the ligand.

1. Deactivate morph conformation.
2. Move the ligand to show it as “flying”.
3. Use Movie Recorder and make the ligand fly from the upper-left corner into its binding pocket during the morph.
4. Play the morph movie from frame 1 to 21 while recording.
5. Stop recording and click Make Movie.

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5. Coloring and labeling volumes

1. Open EMDB ID: 1283 (RNA Polymerase II).
2. View in mesh style.
3. Tools → Volume Data → Volume Tracer
4. Click the mouse middle button to label a region (e.g., stalk of RNA Polymerase II).
5. Label other regions similarly.
6. Change color of each region using marker color in the Volume Tracer window.
7. Tools → Volume Data → Color Zone
8. Set color radius to 20 and click Color.
9. Display the map in surface style (Volume Viewer window).
10. To label the volumes:
    • Utilities → 2D Labels
11. Click on the graphics screen where you want the label.
12. In the 2D Labels window:
    • Type the label text
    • Set label color using the color option at the bottom