From 03c4c88d6117d3e6ed933535a533b51719b3f896 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicolas-Fr=C3=A9d=C3=A9ric=20Lipp=2C=20PhD?=
 <40916571+NicoFrL@users.noreply.github.com>
Date: Mon, 22 Jul 2024 23:33:15 -0700
Subject: [PATCH 1/2] Update coloraf.py

An updated version for more reliability
---
 coloraf.py | 28 ++++++++++++++++++----------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/coloraf.py b/coloraf.py
index f631fbd..2907e25 100644
--- a/coloraf.py
+++ b/coloraf.py
@@ -1,17 +1,25 @@
 from pymol import cmd
 
 
-def coloraf(selection="all"):
+def AFcolors(selection="all"):
 
     """
     AUTHOR
-    Christian Balbin
-
+    Christian Balbin 
+    
+    ADAPTATION
+    Nicolas-Frederic Lipp
+    
     DESCRIPTION
     Colors Alphafold structures by pLDDT
+    An improved version of the original
+    Prevent exact values of 90, 70, and 50 from not being recolored.
+    Ranges were checked on AFDB to ensure that 90, 70, and 50 match their color scheme, despite the nonsensical model confidence legend available on AFDB website.
+    The colors now match exactly AFDB color scheme
+    Replace 'coloraf' by 'AFcolors'
 
     USAGE
-    coloraf sele
+    AFcolors sele
 
     PARAMETERS
 
@@ -19,11 +27,11 @@ def coloraf(selection="all"):
     The name of the selection/object to color by pLDDT. Default: all
     """
 
-    cmd.color("blue", f"({selection}) and b > 90")
-    cmd.color("cyan", f"({selection}) and b < 90 and b > 70")
-    cmd.color("yellow", f"({selection}) and b < 70 and b > 50")
-    cmd.color("orange", f"({selection}) and b < 50")
+    cmd.color("0x126DFF", f"({selection}) and (b > 90 or b = 90)")
+    cmd.color("0x0ECFF1", f"({selection}) and ((b < 90 and b > 70) or b = 70)")
+    cmd.color("0xF6ED12", f"({selection}) and ((b < 70 and b > 50) or b = 50)")
+    cmd.color("0xEE831D", f"({selection}) and b < 50")
 
 
-cmd.extend("coloraf", coloraf)
-cmd.auto_arg[0]["coloraf"] = [cmd.object_sc, "object", ""]
+cmd.extend("AFcolors", AFcolors)
+cmd.auto_arg[0]["AFcolors"] = [cmd.object_sc, "object", ""]

From 38bc67bec7a9392533e025d7f340ec8e720e2a5b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicolas-Fr=C3=A9d=C3=A9ric=20Lipp=2C=20PhD?=
 <40916571+NicoFrL@users.noreply.github.com>
Date: Tue, 23 Jul 2024 00:08:46 -0700
Subject: [PATCH 2/2] Update coloraf.py

update color scheme precisely
---
 coloraf.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/coloraf.py b/coloraf.py
index 2907e25..c78c95b 100644
--- a/coloraf.py
+++ b/coloraf.py
@@ -27,10 +27,10 @@ def AFcolors(selection="all"):
     The name of the selection/object to color by pLDDT. Default: all
     """
 
-    cmd.color("0x126DFF", f"({selection}) and (b > 90 or b = 90)")
-    cmd.color("0x0ECFF1", f"({selection}) and ((b < 90 and b > 70) or b = 70)")
-    cmd.color("0xF6ED12", f"({selection}) and ((b < 70 and b > 50) or b = 50)")
-    cmd.color("0xEE831D", f"({selection}) and b < 50")
+    cmd.color("0x0053D6", f"({selection}) and (b > 90 or b = 90)")
+    cmd.color("0x64CBF3", f"({selection}) and ((b < 90 and b > 70) or b = 70)")
+    cmd.color("0xFFDB13", f"({selection}) and ((b < 70 and b > 50) or b = 50)")
+    cmd.color("0xFE7D45", f"({selection}) and b < 50")
 
 
 cmd.extend("AFcolors", AFcolors)