From 8bab5be18397fe7995d106ce9b3794cae7785751 Mon Sep 17 00:00:00 2001
From: SunHao <oahsun@outlook.com>
Date: Sat, 8 Nov 2025 23:49:53 +0800
Subject: [PATCH] Add condition to check ignore_op3 for missing atoms
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Honor ignore_op3 at chain start: rebuild 5′ P/OP1/OP2 only when missing and ignore_op3 is False.
---
 rna_tools/rna_tools_lib.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rna_tools/rna_tools_lib.py b/rna_tools/rna_tools_lib.py
index ba7a00048..6456f2bbb 100755
--- a/rna_tools/rna_tools_lib.py
+++ b/rna_tools/rna_tools_lib.py
@@ -1659,7 +1659,7 @@ def get_rnapuzzle_ready(self, renumber_residues=True, fix_missing_atoms=True,
                             p_missing = False
                     logger.debug('p_missing %s' % p_missing)
 
-                    if p_missing and fix_missing_atoms:
+                    if p_missing and fix_missing_atoms and (not ignore_op3):
                         currfn = __file__
                         if currfn == '':
                             path = '.'