From d1acebdf5841982b3825f95d7c9ea09a48f586ad Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Tue, 24 Jan 2023 07:51:00 +0000
Subject: [PATCH] JAL-629 suggest not breaking out of the structure processing
 loop if just one structure has a bunk sequence
 association..

---
 src/jalview/bin/Commands.java |    4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 61ee1be..0c34a16 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -412,7 +412,9 @@ public class Commands
           {
             Console.warn("Could not find sequence for argument --"
                     + Arg.STRUCTURE + "=" + val);
-            break STRUCTURE;
+            // you probably want to continue here, not break
+            // break;
+            continue;
           }
           File structureFile = null;
           if (subId.content != null && subId.content.length() != 0)
-- 
1.7.10.2