From 06cbec6fe80007faeb08d88c20b9ba3e1e65ab79 Mon Sep 17 00:00:00 2001
From: ocrampal <ocrampal@ocrampal.com>
Date: Wed, 15 Apr 2026 17:49:50 +0200
Subject: [PATCH] refractory

---
 neuron/soma.md | 28 ++++++++++++++++++----------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/neuron/soma.md b/neuron/soma.md
index 3a5c36e..c67959c 100644
--- a/neuron/soma.md
+++ b/neuron/soma.md
@@ -84,12 +84,14 @@ container: SOMA
     - SpikeTrainTraces ( contained_in: DAY-N )
 ```
 
-### ms: behaviors
+### ms: SOMA
 
 #### CheckVDB: Context
 
 As dendrites deliver current (VDB​), the soma acts like a capacitor. It "stores" this charge in the form of membrane potential. This contextualizes VGSC-SOMA to open ion channels that let Na+ ions in.
 
+This only applies if not AP, or in other words, SOMA is not in refractory period.
+
 ```Gen
 context: CheckVDB
   contained_by: SOMA
@@ -97,13 +99,13 @@ context: CheckVDB
   in_context: Fixed
   rf: ( active: 60x )
 
-  condition: (VDB fullness)
+  condition: (VDB fullness ) AND NOT AP
     out_context: VDBMax
 
-  condition: (VDB mediumness)
+  condition: ( VDB mediumness ) AND NOT AP
     out_context: VDBMedium 
 
-  condition: (VDB emptiness)
+  condition: ( VDB emptiness ) AND NOT AP
     out_context: VDBLow
 ```
 
@@ -118,7 +120,7 @@ context: CheckSomaSpike
   in_context: Fixed
   rf: ( active: 60x )
 
-  condition: ( Na fullness OR APOngoing )
+  condition: ( Na fullness OR APRefractory )
     out_context: AP
     out_context: bAP
 ```
@@ -151,9 +153,9 @@ episode: ClearNa
   trace: 
 ```
 
-### sec: behaviors
+### sec: SOMA
 
-### min: behaviors
+### min: SOMA
 
 #### VGSC-SOMA-TUN: Tuner
 
@@ -208,7 +210,9 @@ container: VGSC-SOMA-H
 
 ```
 
-### Episode1
+### sec: VGSC-SOMA-H
+
+#### Episode1
 
 ```Gen
 episode: ??
@@ -231,7 +235,9 @@ container: VGSC-SOMA-M
 
 ```
 
-### Episode2
+### sec: VGSC-SOMA-M
+
+#### Episode2
 
 ```Gen
 episode: ??
@@ -254,7 +260,9 @@ container: VGSC-SOMA-M
 
 ```
 
-### Episode3
+### sec: VGSC-SOMA-L
+
+#### Episode3
 
 ```Gen
 episode: ??