From e184f1c1dbdef0050cfd419a91c68ffd4638acfd Mon Sep 17 00:00:00 2001
From: Ben Soares <bsoares@dundee.ac.uk>
Date: Mon, 6 Jun 2022 19:56:53 +0100
Subject: [PATCH] JAL-4020 Added the +2 arg for PyMOLWin.exe allowing older
 versions of PyMOL

---
 src/jalview/ext/pymol/PymolManager.java |   11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/jalview/ext/pymol/PymolManager.java b/src/jalview/ext/pymol/PymolManager.java
index 358e360..1def866 100644
--- a/src/jalview/ext/pymol/PymolManager.java
+++ b/src/jalview/ext/pymol/PymolManager.java
@@ -32,11 +32,13 @@ import java.net.URL;
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Locale;
 
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.gui.Preferences;
 import jalview.structure.StructureCommandI;
+import jalview.util.Platform;
 
 public class PymolManager
 {
@@ -110,7 +112,7 @@ public class PymolManager
       {
         for (String path : new String[] { "Schrodinger\\PyMOL2", "PyMOL" })
         {
-          for (String binary : new String[] { "PyMOLWinWithConsole.bat" })
+          for (String binary : new String [] {"PyMOLWinWithConsole.bat", "PyMOLWin.exe"})
           {
             pathList.add(String.format("%s\\%s\\%s", root, path, binary));
           }
@@ -269,8 +271,15 @@ public class PymolManager
         }
         List<String> args = new ArrayList<>();
         args.add(pymolPath);
+        
+        // Windows PyMOLWin.exe needs an extra argument
+        if (Platform.isWin() && pymolPath.toLowerCase(Locale.ROOT).endsWith("\\pymolwin.exe"))
+        {
+          args.add("+2");
+        }
         args.add("-R"); // https://pymolwiki.org/index.php/RPC
         ProcessBuilder pb = new ProcessBuilder(args);
+        Console.debug("Running PyMOL as "+String.join(" ", pb.command()));
         pymolProcess = pb.start();
         error = "";
         break;
-- 
1.7.10.2