Chimera Tutorial (AMPC)

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Based on Powers & Shoichet 2002 paper on characterizing the AMPC binding site:

Characterizing the β-lactamase binding site Chimera tutorial

by Reed Stein, 2015 for course at UCSF.

1. Open Chimera

2. Select an atom or residue by holding CTRL and clicking

3. Rotate the protein by clicking anywhere on the protein and swiping on the trackpad

4. Zoom in/out by clicking anywhere with two fingers and swiping the trackpad

5. Translate the protein by clicking on it with three fingers and swiping the trackpad

6. Favorites → Command Line

7. Type “open 1L2S” on the command line. To select chain A, type “sel :.a”. (Alternatively, Select → Chain → A. Objects that are selected are highlighted in green.)

8. To delete chain A, type “del sel” (Actions → Atoms/Bonds → delete)

9. To center the protein, type “focus” (Actions → focus)

10. To select the catalytic residue, type “sel :64” (Favorites → Sequence. Select residue 64 by clicking and dragging the cursor over the residue.)

11. To display the catalytic residue, type “disp sel” (Actions → Atoms/Bonds → show)

12. To color the catalytic residue green, type “col green sel” (Actions → Color → green)

13. To select the hydrophobic binding site, type “sel :119,293” (Refer to #10)

14. To display the hydrophobic binding site, type “disp sel” (Actions → Atoms/Bonds → show)

15. To color the hydrophobic binding site yellow, type “col yellow sel” (Actions → Color → yellow)

16. The same commands in 10-12 and 13-15 can be used to define the other binding site hot spots:

  • Amide/Aryl: residues 120, 152, and 221, cornflower blue
  • Carbonyl/Hydroxyl: residues 150 and 318, magenta
  • Primary carboxylate site: residues 346, 349, red
  • Water binding sites: residues 61, 319, 322, 215, and 403-405, cyan

17. To represent the water molecules as “ball & stick”, type “rep bs :403-405” (Actions → Atoms/Bonds → ball & stick after selecting these water molecules)

18. To show the molecular surface, type “surface” (Actions → surface → show)