From e4b81015d0a2df4864b63c80f6554871652d8e1e Mon Sep 17 00:00:00 2001
From: Louis Smith <>
Date: Wed, 13 May 2026 18:05:21 -0400
Subject: [PATCH] index and id were swapped in translation from GEMMI API.

---
 src/mmcif.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mmcif.cpp b/src/mmcif.cpp
index 0b27c6124..5b3f718ee 100644
--- a/src/mmcif.cpp
+++ b/src/mmcif.cpp
@@ -51,8 +51,8 @@ namespace loos {
                 std::string res_entity_id = residue.entity_id;
                 for (auto atom:residue.atoms) {
                     loos::pAtom pa(new loos::Atom);
-                    pa->index(atom.serial);
-                    pa->id(atom_index);
+                    pa->index(atom_index);
+                    pa->id(atom.serial);  // from gemmi, comes from _atom_site.id in CIF records.
                     pa->name(atom.name);
                     pa->PDBelement(atom.element.name());
                     pa->coords().x(atom.pos.x);