In https://www.rcsb.org/structure/4YXG LYS 148 doesn't have a C-alpha carbon solved, only the C and O atoms are solved.
ATOM 2955 N VAL B 147 -3.594 -19.441 14.168 1.00 34.28 N
ATOM 2956 CA VAL B 147 -2.519 -18.538 14.505 1.00 34.00 C
ATOM 2957 C VAL B 147 -1.254 -19.343 14.398 1.00 34.01 C
ATOM 2958 O VAL B 147 -0.294 -18.848 13.842 1.00 34.02 O
ATOM 2959 CB VAL B 147 -2.678 -17.797 15.865 1.00 20.00 C
ATOM 2960 CG2 VAL B 147 -3.996 -17.077 15.968 1.00 20.00 C
ATOM 2961 C LYS B 148 0.686 -22.003 13.154 1.00 42.88 C
ATOM 2962 O LYS B 148 1.735 -21.355 13.201 1.00 43.55 O
ATOM 2963 N ALA B 149 -0.290 -21.745 12.288 1.00 42.00 N
ATOM 2964 CA ALA B 149 -0.095 -21.900 10.852 1.00 41.73 C
ATOM 2965 C ALA B 149 0.722 -20.748 10.267 1.00 43.02 C
ATOM 2966 O ALA B 149 1.614 -20.978 9.451 1.00 43.31 O
ATOM 2967 CB ALA B 149 -1.434 -22.015 10.139 1.00 41.47 C
ATOM 2968 N PHE B 150 0.425 -19.519 10.688 1.00 43.24 N
The coordinate that is extracted for this residue is therefore (0,0,0).
Same case for other atoms in the same structure.
We should probably skip these atoms completely and threat them just like residue index jumps.
We have code for this for hetatoms already.
In https://www.rcsb.org/structure/4YXG LYS 148 doesn't have a C-alpha carbon solved, only the C and O atoms are solved.
The coordinate that is extracted for this residue is therefore (0,0,0).
Same case for other atoms in the same structure.
We should probably skip these atoms completely and threat them just like residue index jumps.
We have code for this for hetatoms already.