diff --git a/.ssh/config b/.ssh/config
deleted file mode 100644
index 8ba3dad..0000000
--- a/.ssh/config
+++ /dev/null
@@ -1,25 +0,0 @@
-Host *
-    ForwardX11 yes
-    PermitLocalCommand yes
-    #LocalCommand tar c -C${HOME} --exclude="dotfiles/.git" --exclude=".zim/.git" dotfiles .zim | ssh -o PermitLocalCommand=no %n "tar mx -C${HOME}; bash ~/dotfiles/dotfiles_setup.sh  ; chsh -s /bin/zsh" 
-
-Host summonerapi
-	HostName 46.4.78.43
-
-Host biodata0
-	User bauer
-    HostName biodata0.compbiol.bio.tu-darmstadt.de
-
-Host bioclust
-	User bauer
-	HostName bioclust.bio.tu-darmstadt.de
-
-Host bioinfo4
-    HostName 10.0.0.4
-	User bauer
-    ProxyCommand ssh -q biodata0 nc -q0 %h 22
-
-Host lcluster?*
-  User yg38ymab
-  ForwardX11 yes
-  HostName %h.hrz.tu-darmstadt.de
diff --git a/dotfiles.sh b/dotfiles.sh
new file mode 100755
index 0000000..19c52db
--- /dev/null
+++ b/dotfiles.sh
@@ -0,0 +1,57 @@
+#!/bin/bash
+
+
+PROFILE_BASE_DIR=$HOME/.dotfiles/profiles
+
+# Link files of a single profile
+link_profile() {
+    profile=$1
+    profile_dir=${PROFILE_BASE_DIR}/$profile
+    
+    
+    if [ ! -d $profile_dir ]; then
+    	echo "$profile does not exist"
+		exit 1
+	else
+		echo "Linking files from profile $profile"
+	fi
+
+	cd $profile_dir
+	# Find all files to link
+	for file in `find . -type f | cut -c 3- | grep -v "^$"`; do
+		dir=$(dirname "${file}")
+		src=`pwd`/$file
+		dst_dir=$HOME/$dir
+		dst=$HOME/$file
+		
+		# create folder if not exist
+		if [ ! -d "$dst_dir" ]; then
+			echo "Creating destination direcory $dst_dir"
+			mkdir -p $dst_dir
+		fi
+
+		# link file
+		echo "Linking $src to $dst"
+		if [ -f "${dst}" ] || [ -L "${dst}" ]; then
+			echo "$dst_file esists. Override? [y/N]"
+			read response
+			if [ "$response" == 'y' ] || [ "$response" == 'Y' ] \
+				|| [ "$response" == 'yes' ] || [ "$response" == 'Yes' ]; then
+				ln -sf $src $dst
+			else
+				echo "Skipping $file"
+			fi
+		else
+			ln -s $src $dst	
+		fi
+	done
+}
+
+# link profiles
+if [ "$1" == "link" ]; then
+	shift
+	while [ "$1" != "" ]; do
+		link_profile $1
+		shift
+	done
+fi 
\ No newline at end of file
diff --git a/dotfiles_setup.sh b/dotfiles_setup.sh
deleted file mode 100755
index 0180853..0000000
--- a/dotfiles_setup.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/bash
-dir="${HOME}/dotfiles"
-conffolder="${HOME}/.config"
-
-dotfiles=(".vimrc" ".vim" ".vimrc" ".zshrc" ".zshrc_functions" ".zim" ".zimrc" ".gitconfig")
-for dotfile in "${dotfiles[@]}"; do
-	ln -sf $dir/$dotfile ${HOME}/${dotfile}
-done
-
-# fonts
-mkdir -p ~/.config/fontconfig
-ln -sf $dir/.config/fontconfig/fonts.conf $conffolder/fontconfig/fonts.conf
-
-# matplotlib
-ln -sf $dir/.config/matplotlib ~/.config/matplotlib
diff --git a/install.sh b/install.sh
new file mode 100755
index 0000000..4c7d965
--- /dev/null
+++ b/install.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+# Make ZSH the default shell environment
+if [ `cat /etc/passwd | grep $USER | awk -F ':' '{print $7}'` != "/bin/zsh" ]; then
+	echo "Changing shell to zsh"
+	chsh -s $(which zsh)
+fi
+
+# linking base stuff
+$HOME/.dotfiles/dotfiles.sh link base  
diff --git a/.config/fontconfig/fonts.conf b/profiles/base/.config/fontconfig/fonts.conf
similarity index 100%
rename from .config/fontconfig/fonts.conf
rename to profiles/base/.config/fontconfig/fonts.conf
diff --git a/.gitconfig b/profiles/base/.gitconfig
similarity index 100%
rename from .gitconfig
rename to profiles/base/.gitconfig
diff --git a/.vimrc b/profiles/base/.vimrc
similarity index 100%
rename from .vimrc
rename to profiles/base/.vimrc
diff --git a/.zimrc b/profiles/base/.zimrc
similarity index 100%
rename from .zimrc
rename to profiles/base/.zimrc
diff --git a/.zshrc b/profiles/base/.zshrc
similarity index 100%
rename from .zshrc
rename to profiles/base/.zshrc
diff --git a/.config/i3/autoxrandr b/profiles/i3/.config/i3/autoxrandr
similarity index 100%
rename from .config/i3/autoxrandr
rename to profiles/i3/.config/i3/autoxrandr
diff --git a/.config/i3/config b/profiles/i3/.config/i3/config
similarity index 100%
rename from .config/i3/config
rename to profiles/i3/.config/i3/config
diff --git a/.config/i3/scripts/change_monitor.sh b/profiles/i3/.config/i3/scripts/change_monitor.sh
similarity index 100%
rename from .config/i3/scripts/change_monitor.sh
rename to profiles/i3/.config/i3/scripts/change_monitor.sh
diff --git a/.config/i3/scripts/cpu_usage b/profiles/i3/.config/i3/scripts/cpu_usage
similarity index 100%
rename from .config/i3/scripts/cpu_usage
rename to profiles/i3/.config/i3/scripts/cpu_usage
diff --git a/.config/i3/scripts/current_track b/profiles/i3/.config/i3/scripts/current_track
similarity index 100%
rename from .config/i3/scripts/current_track
rename to profiles/i3/.config/i3/scripts/current_track
diff --git a/.config/i3/scripts/disk b/profiles/i3/.config/i3/scripts/disk
similarity index 100%
rename from .config/i3/scripts/disk
rename to profiles/i3/.config/i3/scripts/disk
diff --git a/.config/i3/scripts/exit_menu b/profiles/i3/.config/i3/scripts/exit_menu
similarity index 100%
rename from .config/i3/scripts/exit_menu
rename to profiles/i3/.config/i3/scripts/exit_menu
diff --git a/.config/i3/scripts/gpu b/profiles/i3/.config/i3/scripts/gpu
similarity index 100%
rename from .config/i3/scripts/gpu
rename to profiles/i3/.config/i3/scripts/gpu
diff --git a/.config/i3/scripts/keyboard_layout b/profiles/i3/.config/i3/scripts/keyboard_layout
similarity index 100%
rename from .config/i3/scripts/keyboard_layout
rename to profiles/i3/.config/i3/scripts/keyboard_layout
diff --git a/.config/i3/scripts/load_average b/profiles/i3/.config/i3/scripts/load_average
similarity index 100%
rename from .config/i3/scripts/load_average
rename to profiles/i3/.config/i3/scripts/load_average
diff --git a/.config/i3/scripts/memory b/profiles/i3/.config/i3/scripts/memory
similarity index 100%
rename from .config/i3/scripts/memory
rename to profiles/i3/.config/i3/scripts/memory
diff --git a/.config/i3/scripts/openvpn b/profiles/i3/.config/i3/scripts/openvpn
similarity index 100%
rename from .config/i3/scripts/openvpn
rename to profiles/i3/.config/i3/scripts/openvpn
diff --git a/.config/i3/scripts/shutdown_menu b/profiles/i3/.config/i3/scripts/shutdown_menu
similarity index 100%
rename from .config/i3/scripts/shutdown_menu
rename to profiles/i3/.config/i3/scripts/shutdown_menu
diff --git a/.config/i3/scripts/song.awk b/profiles/i3/.config/i3/scripts/song.awk
similarity index 100%
rename from .config/i3/scripts/song.awk
rename to profiles/i3/.config/i3/scripts/song.awk
diff --git a/.config/i3/scripts/spotify.py b/profiles/i3/.config/i3/scripts/spotify.py
similarity index 100%
rename from .config/i3/scripts/spotify.py
rename to profiles/i3/.config/i3/scripts/spotify.py
diff --git a/.config/i3/scripts/spotify_control b/profiles/i3/.config/i3/scripts/spotify_control
similarity index 100%
rename from .config/i3/scripts/spotify_control
rename to profiles/i3/.config/i3/scripts/spotify_control
diff --git a/.config/i3/scripts/spotify_control.bck b/profiles/i3/.config/i3/scripts/spotify_control.bck
similarity index 100%
rename from .config/i3/scripts/spotify_control.bck
rename to profiles/i3/.config/i3/scripts/spotify_control.bck
diff --git a/.config/i3/scripts/ssd b/profiles/i3/.config/i3/scripts/ssd
similarity index 100%
rename from .config/i3/scripts/ssd
rename to profiles/i3/.config/i3/scripts/ssd
diff --git a/.config/i3/scripts/tmux b/profiles/i3/.config/i3/scripts/tmux
similarity index 100%
rename from .config/i3/scripts/tmux
rename to profiles/i3/.config/i3/scripts/tmux
diff --git a/.config/i3/scripts/volume b/profiles/i3/.config/i3/scripts/volume
similarity index 100%
rename from .config/i3/scripts/volume
rename to profiles/i3/.config/i3/scripts/volume
diff --git a/.config/i3/scripts/volume-pulseaudio b/profiles/i3/.config/i3/scripts/volume-pulseaudio
similarity index 100%
rename from .config/i3/scripts/volume-pulseaudio
rename to profiles/i3/.config/i3/scripts/volume-pulseaudio
diff --git a/.config/i3/scripts/volume_1 b/profiles/i3/.config/i3/scripts/volume_1
similarity index 100%
rename from .config/i3/scripts/volume_1
rename to profiles/i3/.config/i3/scripts/volume_1
diff --git a/.config/i3/workspace-9.json b/profiles/i3/.config/i3/workspace-9.json
similarity index 100%
rename from .config/i3/workspace-9.json
rename to profiles/i3/.config/i3/workspace-9.json
diff --git a/.config/i3/xrandr.sh b/profiles/i3/.config/i3/xrandr.sh
similarity index 100%
rename from .config/i3/xrandr.sh
rename to profiles/i3/.config/i3/xrandr.sh
diff --git a/.config/polybar/config b/profiles/i3/.config/polybar/config
similarity index 100%
rename from .config/polybar/config
rename to profiles/i3/.config/polybar/config
diff --git a/.config/polybar/gpu.sh b/profiles/i3/.config/polybar/gpu.sh
similarity index 100%
rename from .config/polybar/gpu.sh
rename to profiles/i3/.config/polybar/gpu.sh
diff --git a/.config/polybar/polybar.sh b/profiles/i3/.config/polybar/polybar.sh
similarity index 100%
rename from .config/polybar/polybar.sh
rename to profiles/i3/.config/polybar/polybar.sh
diff --git a/.config/polybar/spotify.py b/profiles/i3/.config/polybar/spotify.py
similarity index 100%
rename from .config/polybar/spotify.py
rename to profiles/i3/.config/polybar/spotify.py
diff --git a/profiles/pymol/.pymol/.pymol b/profiles/pymol/.pymol/.pymol
new file mode 120000
index 0000000..210ed3d
--- /dev/null
+++ b/profiles/pymol/.pymol/.pymol
@@ -0,0 +1 @@
+/home/bauer/dotfiles/.pymol
\ No newline at end of file
diff --git a/.pymol/pymol-edu-license.lic b/profiles/pymol/.pymol/pymol-edu-license.lic
similarity index 100%
rename from .pymol/pymol-edu-license.lic
rename to profiles/pymol/.pymol/pymol-edu-license.lic
diff --git a/.pymol/startup/Draw_Protein_Dimensions.py b/profiles/pymol/.pymol/startup/Draw_Protein_Dimensions.py
similarity index 100%
rename from .pymol/startup/Draw_Protein_Dimensions.py
rename to profiles/pymol/.pymol/startup/Draw_Protein_Dimensions.py
diff --git a/.pymol/startup/anglebetweenhelices.py b/profiles/pymol/.pymol/startup/anglebetweenhelices.py
similarity index 100%
rename from .pymol/startup/anglebetweenhelices.py
rename to profiles/pymol/.pymol/startup/anglebetweenhelices.py
diff --git a/.pymol/startup/axes.py b/profiles/pymol/.pymol/startup/axes.py
similarity index 100%
rename from .pymol/startup/axes.py
rename to profiles/pymol/.pymol/startup/axes.py
diff --git a/.pymol/startup/center_of_mass.py b/profiles/pymol/.pymol/startup/center_of_mass.py
similarity index 100%
rename from .pymol/startup/center_of_mass.py
rename to profiles/pymol/.pymol/startup/center_of_mass.py
diff --git a/.pymol/startup/centroid.py b/profiles/pymol/.pymol/startup/centroid.py
similarity index 100%
rename from .pymol/startup/centroid.py
rename to profiles/pymol/.pymol/startup/centroid.py
diff --git a/.pymol/startup/color_h.py b/profiles/pymol/.pymol/startup/color_h.py
similarity index 100%
rename from .pymol/startup/color_h.py
rename to profiles/pymol/.pymol/startup/color_h.py
diff --git a/.pymol/startup/dssp_stride.py b/profiles/pymol/.pymol/startup/dssp_stride.py
similarity index 100%
rename from .pymol/startup/dssp_stride.py
rename to profiles/pymol/.pymol/startup/dssp_stride.py
diff --git a/.pymol/startup/propka.py b/profiles/pymol/.pymol/startup/propka.py
similarity index 100%
rename from .pymol/startup/propka.py
rename to profiles/pymol/.pymol/startup/propka.py
diff --git a/.pymol/startup/show_contact_map.py b/profiles/pymol/.pymol/startup/show_contact_map.py
similarity index 100%
rename from .pymol/startup/show_contact_map.py
rename to profiles/pymol/.pymol/startup/show_contact_map.py
diff --git a/.pymol/startup/spectrum_states.py b/profiles/pymol/.pymol/startup/spectrum_states.py
similarity index 100%
rename from .pymol/startup/spectrum_states.py
rename to profiles/pymol/.pymol/startup/spectrum_states.py
diff --git a/.pymol/startup/visualize_dca_scores.py b/profiles/pymol/.pymol/startup/visualize_dca_scores.py
similarity index 100%
rename from .pymol/startup/visualize_dca_scores.py
rename to profiles/pymol/.pymol/startup/visualize_dca_scores.py
diff --git a/.pymolrc b/profiles/pymol/.pymolrc
similarity index 100%
rename from .pymolrc
rename to profiles/pymol/.pymolrc