commit

profiles/base/.local/share/marker/user_commands.txt

@@ -1 +1,2 @@
-cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/gromacs-2019.1/ -DCMAKE_C_COMPILER=/usr/bin/gcc-4.9 -DCMAKE_CXX_COMPILER=/usr/bin/g++-4.9##gmx_compile
+cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/gromacs-2019.1/ -DCMAKE_C_COMPILER=/usr/bin/gcc-4.9 -DCMAKE_CXX_COMPILER=/usr/bin/g++-4.9##gmx_compile
+git clone git@git.compbiol.bio.tu-darmstadt.de:Daniel/md-template.git sim##md-template

profiles/desktop/.config/terminator/config

@@ -0,0 +1,25 @@
+[global_config]
+  enabled_plugins = InactivityWatch, ActivityWatch, TerminalShot, LaunchpadCodeURLHandler, APTURLHandler, LaunchpadBugURLHandler
+  suppress_multiple_term_dialog = True
+[keybindings]
+[layouts]
+  [[default]]
+    [[[child1]]]
+      parent = window0
+      type = Terminal
+    [[[window0]]]
+      parent = ""
+      type = Window
+[plugins]
+[profiles]
+  [[default]]
+    allow_bold = False
+    copy_on_selection = True
+    cursor_color = "#aaaaaa"
+    font = Hack 14
+    palette = "#282828:#cc241d:#98971a:#d79921:#458588:#b16286:#689d6a:#a89984:#928374:#fb4934:#b8bb26:#fabd2f:#83a598:#d3869b:#8ec07c:#ebdbb2"
+    rewrap_on_resize = False
+    scrollback_infinite = True
+    scrollback_lines = 5000
+    show_titlebar = False
+    use_system_font = False

profiles/pymol/.pymolrc

@@ -5,6 +5,7 @@ set fetch_path, /tmp
 log_open /tmp/pymol_log.pml
 set retain_order
 
+
 # interface
 set overlay, 1
 
@@ -38,9 +39,11 @@ set surface_quality, 1
 set ray_trace_mode, 0
 
 set valence, 0
+set cartoon_gap_cutoff, 0
 set cartoon_side_chain_helper, 1
 set cartoon_discrete_colors, on
 
-alias clean, hide everything, hydrogen
+alias clean, hide everything, hydrogen or n. 1M* or n. 2M*
+alias sf_as_sticks, show_as sticks, resid 479-483; clean