diff --git a/moltemplate/scripts/moltemplate.sh b/moltemplate/scripts/moltemplate.sh
index faf535f0..bd51f64b 100755
--- a/moltemplate/scripts/moltemplate.sh
+++ b/moltemplate/scripts/moltemplate.sh
@@ -6,7 +6,7 @@
 # Copyright (c) 2013
 
 G_PROGRAM_NAME="moltemplate.sh"
-G_VERSION="2.16.0"
+G_VERSION="2.16.1"
 G_DATE="2020-2-21"
 
 echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2
diff --git a/moltemplate/ttree_matrix_stack.py b/moltemplate/ttree_matrix_stack.py
index b7b35bd4..e0d9ac58 100644
--- a/moltemplate/ttree_matrix_stack.py
+++ b/moltemplate/ttree_matrix_stack.py
@@ -401,7 +401,7 @@ def CommandsToMatrix(text,  # text containing affine transformation commands
                     AffineCompose(Mtmp, moveCentBack, Mdest)
                     CopyMat(Mdest, Mtmp)
 
-            if transform_str.find('matrix(') == 0:
+            elif transform_str.find('matrix(') == 0:
                 i_paren_close = transform_str.find(')')
                 if i_paren_close == -1:
                     i_paren_close = len(transform_str)
diff --git a/setup.py b/setup.py
index 2cc88e11..64351d1b 100644
--- a/setup.py
+++ b/setup.py
@@ -45,9 +45,9 @@
 
   url='https://github.com/jewettaij/moltemplate',
 
-  download_url='https://github.com/jewettaij/moltemplate/archive/v2.16.0.zip',
+  download_url='https://github.com/jewettaij/moltemplate/archive/v2.16.1.zip',
 
-  version='2.16.0',
+  version='2.16.1',
 
   keywords=['simulation', 'LAMMPS', 'molecule editor', 'molecule builder',
             'ESPResSo'],