From b460eb596ded433669873cbb161e8048b66a6417 Mon Sep 17 00:00:00 2001
From: Daniel Bauer <bauer@cbs.tu-darmstadt.de>
Date: Sun, 24 Mar 2019 11:42:05 +0100
Subject: [PATCH] pymol

---
 profiles/pymol/.pymolrc | 64 ++++++++++++++++++++++++++++++++++-------
 1 file changed, 53 insertions(+), 11 deletions(-)

diff --git a/profiles/pymol/.pymolrc b/profiles/pymol/.pymolrc
index 6cf75c2..242a07e 100644
--- a/profiles/pymol/.pymolrc
+++ b/profiles/pymol/.pymolrc
@@ -1,21 +1,63 @@
+# general environment
+bg_color white
+space cmyk
 set fetch_path, /tmp
-set async_builds, on
-set max_threads, 16
-set cache_mode 
-
-set opaque_background, 0
 log_open /tmp/pymol_log.pml
-set cartoon_side_chain_helper, 1
-set cartoon_highlight_color, grey50
+set retain_order
 
+
+# interface
+set overlay, 1
+set internal_gui_control_size, 10
+set display_scale_factor, 2
+
+# performance
+set async_builds, on
+set max_threads, 8
+set cache_mode
+set defer_builds_mode, 3
+set hash_max, 500
+
+# shortcuts
 set_key F1, as lines, solvent
 set_key F2, hide everything, solvent
 set_key F3, as spheres, inorganic and (n. NA or n. K or n. CL or n. CA or n. XE or n. RN)
 set_key F4, hide everything, inorganic and (n. NA or n. K or n. CL or n. CA or n. XE or n. RN)
 set_key F5, as sticks, organic
 set_key F6, hide everything, organic
-
-set_key F9, set orthoscopic
-set_key F10, set orthoscopic, off
-set_key F11, ray
+set_key F9, set depth_cue
+set_key F10, set depth_cue, off
+set_key F11, ray 800,800
 set_key F12, ray 1600,1600
+
+#Extending colors with color-blindness friendly color palette
+#References:
+#http://jfly.iam.u-tokyo.ac.jp/html/color_cb/#pallet
+#https://personal.sron.nl/~pault/colourschemes.pdf
+set_color cb_blue, [51, 34, 136]
+set_color cb_tan, [221, 204, 119]
+set_color cb_lightblue, [136, 204, 238]
+set_color cb_green, [17, 119, 51]
+set_color cb_teal, [68, 170, 153]
+set_color cb_gold, [153, 153, 51]
+set_color cb_salmon, [204, 102, 119]
+set_color cb_red, [136, 34, 85]
+set_color cb_pink, [170, 68, 153]
+
+# raytrace
+set depth_cue, 0
+set ray_opaque_background, false
+set orthoscopic, 0
+set ray_shadow, false 
+set spec_reflect, 0
+set antialias, 0
+set surface_quality, 1
+set ray_trace_mode, 0
+
+set valence, 0
+set cartoon_side_chain_helper, 1
+set cartoon_discrete_colors, on
+
+alias clean, hide everything, hydrogen
+
+