Besides the overlapping numbering which can be solved using pdb-tools, sometimes the PDB has multiple conformations of the same residue, for example:
ATOM 1 N THR A 1 17.047 14.099 3.625 1.00 13.79 N
ATOM 2 CA THR A 1 16.967 12.784 4.338 1.00 10.80 C
ATOM 3 C THR A 1 15.685 12.755 5.133 1.00 9.19 C
ATOM 4 O THR A 1 15.268 13.825 5.594 1.00 9.85 O
ATOM 5 CB THR A 1 18.170 12.703 5.337 1.00 13.02 C
ATOM 6 OG1 THR A 1 19.334 12.829 4.463 1.00 15.06 O
ATOM 7 CG2 THR A 1 18.150 11.546 6.304 1.00 14.23 C
ATOM 8 N ATHR A 1 15.115 11.555 5.265 1.00 7.81 N
ATOM 9 CA ATHR A 1 13.856 11.469 6.066 1.00 8.31 C
ATOM 10 C ATHR A 1 14.164 10.785 7.379 1.00 5.80 C
ATOM 11 O ATHR A 1 14.993 9.862 7.443 1.00 6.94 O
ATOM 12 CB ATHR A 1 12.732 10.711 5.261 1.00 10.32 C
ATOM 13 OG1ATHR A 1 13.308 9.439 4.926 1.00 12.81 O
Here there are multiple possibilities for the side-chain conformation of aminoacid 1, you should open the structure on PyMol and identify which is the best conformation.
Let’s say you want to remove conformation A of residues 1, what you need to do is open it in a code editor such as Notepad++ (do not use MS Word, Wordpad, OpenOffice, etc) and manually remove the lines for duplicated residues (ATHR):
ATOM 1 N THR A 1 17.047 14.099 3.625 1.00 13.79 N
ATOM 2 CA THR A 1 16.967 12.784 4.338 1.00 10.80 C
ATOM 3 C THR A 1 15.685 12.755 5.133 1.00 9.19 C
ATOM 4 O THR A 1 15.268 13.825 5.594 1.00 9.85 O
ATOM 5 CB THR A 1 18.170 12.703 5.337 1.00 13.02 C
ATOM 6 OG1 THR A 1 19.334 12.829 4.463 1.00 15.06 O
ATOM 7 CG2 THR A 1 18.150 11.546 6.304 1.00 14.23 C