Apoferritin 11638
Versions:
OccuPy 1.7.0
ChimeraX 1.4 (2022-06-03)
Setup
Get the PDB for annotation
$ wget https://files.rcsb.org/download/7A4M.pdb
In OccuPy
- Fetch EMDB 11638
- Set extra option "Naive normalization" = checked
- Estimate scale
- Launch ChimeraX (open chimX_emd_11638.cxc through ChimeraX)
In chimeraX
Open 7A4M.pdb, here as #4
hide cartoon
hide atoms
select #4:95-104,48-58
show sel
view sel
molmap sel 8
vol #5 level 0.113
vol mask #1 surfaces #5
vol gaussian #6 sdev 0.5
hide #5
volume #7 color #00000099
scale_color #7 #2
select H
hide sel
surface dust #6 size 2
color #4 #bababa transparency 0
color byhetero
graphics silhouettes true
Other Views
Waters
In OccuPy
- Set extra option "Naive normalization" = unchecked
- Set input lowpass = 3Å
- Set occupancy = checked
- Estimate scale
- Set sigmoid power = 30 , pivot = 0.05
- Modify map
- Launch ChimeraX (open chimX_emd_11638.cxc through ChimeraX)