JAL-1757 match only first altloc CA in PDB structure for superposition

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 45fc378..50e156f 100644 (file)
--- 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 = "";