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GluK2/K5 kainate receptor 23015

Versions:

OccuPy 1.8.0rc2
ChimeraX 1.4 (2022-06-03)

In OccuPy

  1. Fetch EMDB 23015.
  2. Set the input lowpass to 5Å. This is too low to provide a reasonable occupancy estimate, but it's the value used in the paper to show modification when occupancy is under-estimated. A better value for fidelity is probably around 10Å.
  3. Set scale occupancy = checked
  4. Click "Estimate scale"
  5. Enable Amplification and set Power=3
  6. Enable Attenuation and set Power=3
  7. Enable Sigmoid and set Power=30 and Pivot=0.50
  8. Click "Modify Map"
  9. Launch ChimeraX (open chimX_emd_23015.cxc through ChimeraX)

In chimeraX

Use the command occupy_level <value> to set the input and all modifies maps at the same threshold value.

view matrix camera 1.4173e-16,-4.3526e-16,-1,-289.68,0.99756,0.069756,1.1102e-16,164.34,0.069756,-0.99756,4.4409e-16,199.43
occupy_level 0.65

level 0.65 level 0.30