X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=50e156f91d3daf00323b4fe8ac820fae4c4093b4;hb=85937698cb3a6d1fb8be1cfa7a1677e632da7be9;hp=45fc37849f6e17345c558a25924649d6d167cb22;hpb=17fe82c9d7f9da1b17f3091e4b3992a35e3e411e;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 45fc378..50e156f 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -507,7 +507,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         command.append(1 + pdbfnum);
         command.append(".1} {");
         command.append(1 + refStructure);
-        command.append(".1} SUBSET {*.CA | *.P} ATOMS ");
+        // conformation=1 excludes alternate locations for CA (JAL-1757)
+        command.append(".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
 
         // form the matched pair strings
         String sep = "";