diff --git a/functions/DAlphaBall.gcc b/functions/DAlphaBall.gcc
old mode 100644
new mode 100755
diff --git a/functions/dssp b/functions/dssp
old mode 100644
new mode 100755
diff --git a/install_bindcraft.sh b/install_bindcraft.sh
old mode 100644
new mode 100755
index 89bc7de..4b9d92f
--- a/install_bindcraft.sh
+++ b/install_bindcraft.sh
@@ -46,26 +46,19 @@ SECONDS=0
 
 # set paths needed for installation and check for conda installation
 install_dir=$(pwd)
-CONDA_BASE=$(conda info --base 2>/dev/null) || { echo -e "Error: conda is not installed or cannot be initialised."; exit 1; }
-echo -e "Conda is installed at: $CONDA_BASE"
+env_name="BindCraft"
 
 ### BindCraft install begin, create base environment
 echo -e "Installing BindCraft environment\n"
-$pkg_manager create --name BindCraft python=3.10 -y || { echo -e "Error: Failed to create BindCraft conda environment"; exit 1; }
-conda env list | grep -w 'BindCraft' >/dev/null 2>&1 || { echo -e "Error: Conda environment 'BindCraft' does not exist after creation."; exit 1; }
-
-# Load newly created BindCraft environment
-echo -e "Loading BindCraft environment\n"
-source ${CONDA_BASE}/bin/activate ${CONDA_BASE}/envs/BindCraft || { echo -e "Error: Failed to activate the BindCraft environment."; exit 1; }
-[ "$CONDA_DEFAULT_ENV" = "BindCraft" ] || { echo -e "Error: The BindCraft environment is not active."; exit 1; }
-echo -e "BindCraft environment activated at ${CONDA_BASE}/envs/BindCraft"
+${pkg_manager} create --name $env_name python=3.10 -y || { echo -e "Error: Failed to create BindCraft conda environment"; exit 1; }
+${pkg_manager} env list | grep -w $env_name >/dev/null 2>&1 || { echo -e "Error: Conda environment '${env_name}' does not exist after creation."; exit 1; }
 
 # install required conda packages
-echo -e "Instaling conda requirements\n"
+echo -e "Installing conda requirements\n"
 if [ -n "$cuda" ]; then
-    CONDA_OVERRIDE_CUDA="$cuda" $pkg_manager install pip pandas matplotlib numpy"<2.0.0" biopython scipy pdbfixer seaborn libgfortran5 tqdm jupyter ffmpeg pyrosetta fsspec py3dmol chex dm-haiku flax"<0.10.0" dm-tree joblib ml-collections immutabledict optax jaxlib=*=*cuda* jax cuda-nvcc cudnn -c conda-forge -c nvidia  --channel https://conda.graylab.jhu.edu -y || { echo -e "Error: Failed to install conda packages."; exit 1; }
+    CONDA_OVERRIDE_CUDA="$cuda" $pkg_manager install --name ${env_name} pip pandas matplotlib numpy"<2.0.0" biopython scipy pdbfixer seaborn libgfortran5 tqdm jupyter ffmpeg pyrosetta fsspec py3dmol chex dm-haiku flax"<0.10.0" dm-tree joblib ml-collections immutabledict optax jaxlib=*=*cuda* jax cuda-nvcc cudnn -c conda-forge -c nvidia  --channel https://conda.graylab.jhu.edu -y || { echo -e "Error: Failed to install conda packages."; exit 1; }
 else
-    $pkg_manager install pip pandas matplotlib numpy"<2.0.0" biopython scipy pdbfixer seaborn libgfortran5 tqdm jupyter ffmpeg pyrosetta fsspec py3dmol chex dm-haiku flax"<0.10.0" dm-tree joblib ml-collections immutabledict optax jaxlib jax cuda-nvcc cudnn -c conda-forge -c nvidia  --channel https://conda.graylab.jhu.edu -y || { echo -e "Error: Failed to install conda packages."; exit 1; }
+    $pkg_manager install --name ${env_name} pip pandas matplotlib numpy"<2.0.0" biopython scipy pdbfixer seaborn libgfortran5 tqdm jupyter ffmpeg pyrosetta fsspec py3dmol chex dm-haiku flax"<0.10.0" dm-tree joblib ml-collections immutabledict optax jaxlib jax cuda-nvcc cudnn -c conda-forge -c nvidia  --channel https://conda.graylab.jhu.edu -y || { echo -e "Error: Failed to install conda packages."; exit 1; }
 fi
 
 # make sure all required packages were installed
@@ -74,7 +67,7 @@ missing_packages=()
 
 # Check each package
 for pkg in "${required_packages[@]}"; do
-    conda list "$pkg" | grep -w "$pkg" >/dev/null 2>&1 || missing_packages+=("$pkg")
+    ${pkg_manager} list --name "$env_name" | grep -w "$pkg" >/dev/null 2>&1 || missing_packages+=("$pkg")
 done
 
 # If any packages are missing, output error and exit
@@ -86,10 +79,10 @@ if [ ${#missing_packages[@]} -ne 0 ]; then
     exit 1
 fi
 
-# install ColabDesign
+# Install ColabDesign
 echo -e "Installing ColabDesign\n"
-pip3 install git+https://github.com/sokrypton/ColabDesign.git --no-deps || { echo -e "Error: Failed to install ColabDesign"; exit 1; }
-python -c "import colabdesign" >/dev/null 2>&1 || { echo -e "Error: colabdesign module not found after installation"; exit 1; }
+$pkg_manager run --name ${env_name} pip3 install git+https://github.com/sokrypton/ColabDesign.git --no-deps || { echo -e "Error: Failed to install ColabDesign"; exit 1; }
+$pkg_manager run --name ${env_name} python -c "import colabdesign" >/dev/null 2>&1 || { echo -e "Error: colabdesign module not found after installation"; exit 1; }
 
 # AlphaFold2 weights
 echo -e "Downloading AlphaFold2 model weights \n"
@@ -128,4 +121,4 @@ t=$SECONDS
 echo -e "Successfully finished BindCraft installation!\n"
 echo -e "Activate environment using command: \"$pkg_manager activate BindCraft\""
 echo -e "\n"
-echo -e "Installation took $(($t / 3600)) hours, $((($t / 60) % 60)) minutes and $(($t % 60)) seconds."
\ No newline at end of file
+echo -e "Installation took $(($t / 3600)) hours, $((($t / 60) % 60)) minutes and $(($t % 60)) seconds."