Chimera Tutorial (Delta opioid receptor)

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Delta opioid receptor

By Reed Stein, 2016 PSPG bootcamp 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 4N6H” (delta-opioid receptor bound to the antagonist, naltrindole)

 “sel #0:37-338:HOH,NA,EJ4”
 “sel invert sel”
 “del sel”
 “preset app int 1”
 “background solid white”
 “turn x 1 90”
 “turn y 1 270”
 “center ligand”
 “sel ligand Z<5 & polar”
 “sel sel | :HOH & ligand Z<5”
  “disp sel”
 “rlabel sel”
 “color purple ,l sel”
 “sel sel | #0:EJ4@O??,N??”
 “hbonds selRestrict sel intraRes false intermodel false showDist true color orange”
 “scale 1.02 50; wait; transp 80,r; wait; turn y 1 360”
 “col orange ligand”
 “col byhet ligand”
 “surface ligand”
 “sel ligand Z<5”
 “repr sphere sel”
 “turn y 1 360”
 “repr stick sel”
 “transp 0”
 “sel #0”
 “rangecolor bfactor,r key 0 blue 25 white 50 red sel”
 “sel ligand”
 “~surface sel”
 “~rlabel sel”
 “~hbonds”