What if chain starts with a number different than 1 (people tend to number chain residues in many different ways, even using negative numbers, and they claim they have valid reasons to do so)?

iotbx.pdb.hierarchy has a clear definition of the chain. So I'd suggest adding NH3 to the fist residue of the chain, no matter what that residue number is.

Pavel

Repository : https://github.com/cctbx/cctbx_project/
On branch  : master
Link       : https://github.com/cctbx/cctbx_project/commit/765881e87b5982c3b68e8dcd8c0e00c61c5b5600

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commit 765881e87b5982c3b68e8dcd8c0e00c61c5b5600
Author: dcliebschner <[email protected]>
Date:   Wed Nov 10 14:03:06 2021 -0800

    Reduce2: place NH3 only at residue with resseq 1.

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765881e87b5982c3b68e8dcd8c0e00c61c5b5600
mmtbx/hydrogens/reduce_hydrogen.py    |  19 +-
mmtbx/hydrogens/tst_add_hydrogen.py   | 196 ++++++++---------
mmtbx/hydrogens/tst_add_hydrogen_2.py | 383 ++++++++++++++++------------------
3 files changed, 282 insertions(+), 316 deletions(-)

Diff suppressed because of size. To see it, use:

    git diff-tree --root --patch-with-stat --no-color --ignore-space-at-eol --textconv --ext-diff --cc 765881e87b5982c3b68e8dcd8c0e00c61c5b5600

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