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

1. Fetch EMDB 11638
2. Set extra option "Naive normalization" = checked
3. Estimate scale
4. 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

1. Set extra option "Naive normalization" = unchecked
2. Set input lowpass = 3Å
3. Set occupancy = checked
4. Estimate scale
5. Set sigmoid power = 30 , pivot = 0.05
6. Modify map
7. Launch ChimeraX (open chimX_emd_11638.cxc through ChimeraX)