GluK2/K5 kainate receptor 23015
Versions:
OccuPy 1.8.0rc2
ChimeraX 1.4 (2022-06-03)
In OccuPy
- Fetch EMDB 23015.
- 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.
- Set scale occupancy = checked
- Click "Estimate scale"
- Enable Amplification and set Power=3
- Enable Attenuation and set Power=3
- Enable Sigmoid and set Power=30 and Pivot=0.50
- Click "Modify Map"
- 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