Non-unified processing of cysteine residues

[beautifulpie]

Using pdbfixer to process residues, when adding hydrogens to cysteine residues, some residues are given hydrogens in a deprotonated form. I want a consistent behavior, so I wonder what I should do to achieve that. I have also tried adjusting the pH, but it did not produce the behavior I wanted. It seems to be caused by a disulfide linkage, and I'm wondering if there is any way to ignore it

Below are some examples from that output.

ATOM 961 N CYS E 62 -2.043 124.350 -12.197 1.00 0.00 N
ATOM 962 H CYS E 62 -2.555 125.193 -11.530 1.00 0.00 H
ATOM 963 CA CYS E 62 -2.331 124.560 -13.610 1.00 0.00 C
ATOM 964 HA CYS E 62 -1.700 124.041 -14.474 1.00 0.00 H
ATOM 965 C CYS E 62 -2.405 126.051 -13.924 1.00 0.00 C
ATOM 966 O CYS E 62 -3.387 126.717 -13.598 1.00 0.00 O
ATOM 967 CB CYS E 62 -3.636 123.865 -14.001 1.00 0.00 C
ATOM 968 HB2 CYS E 62 -3.892 123.187 -13.060 1.00 0.00 H
ATOM 969 HB3 CYS E 62 -4.528 124.642 -14.161 1.00 0.00 H
ATOM 970 SG CYS E 62 -3.900 123.722 -15.783 1.00 0.00 S
ATOM 971 HG CYS E 62 -3.368 123.701 -16.834 1.00 0.00 H

ATOM 2049 N CYS E 135 -33.400 102.984 -14.440 1.00 0.00 N
ATOM 2050 H CYS E 135 -32.480 103.628 -14.808 1.00 0.00 H
ATOM 2051 CA CYS E 135 -32.885 101.987 -13.509 1.00 0.00 C
ATOM 2052 HA CYS E 135 -33.393 102.082 -12.443 1.00 0.00 H
ATOM 2053 C CYS E 135 -31.377 102.107 -13.322 1.00 0.00 C
ATOM 2054 O CYS E 135 -30.621 102.151 -14.293 1.00 0.00 O
ATOM 2055 CB CYS E 135 -33.241 100.579 -13.985 1.00 0.00 C
ATOM 2056 HB2 CYS E 135 -34.362 100.204 -13.945 1.00 0.00 H
ATOM 2057 HB3 CYS E 135 -32.453 100.280 -14.829 1.00 0.00 H
ATOM 2058 SG CYS E 135 -32.827 99.273 -12.809 1.00 0.00 S

[peastman]

If there's a disulfide bond, it shouldn't add a hydrogen. That's correct behavior. Can you describe what you're trying to do?