Problem with representation of amino acid sequence when there is incomplete data about icn3d HOT 2 CLOSED

Similar to Cn3D, iCn3D also uses lower-case letter to indicate missing residues, e.g., residues at position 433 in the chain A of PDB 3GVU are missing: https://structure.ncbi.nlm.nih.gov/icn3d/share.html?n6HTtzbaJyaJ8Niu6.
The problem in your example is that the PDB file didn't indicate that the residues 230-234 are missing. The missing residues are specified with "REMARK 465". No missing residues were reported for this structure:
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 475

from icn3d.

You could use NCBI residue number instead of PDB residue number in this case: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1igy&usepdbnum=0 . The parameter "usepdbnum" is 1 (true) by default. The NCBI residue numbers are D215 and C216 for the PDB residue number D229 and C235.

from icn3d.