From 9bdd5401413754ca777823c278933de7cf83643a Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 24 Aug 2017 13:56:14 +0200
Subject: [PATCH] some more info on how the default StructureDB got created
---
extras/data_generation/structure_db/README | 10 ++++++++++
1 file changed, 10 insertions(+)
diff --git a/extras/data_generation/structure_db/README b/extras/data_generation/structure_db/README
index 22731306..ed5115dd 100644
--- a/extras/data_generation/structure_db/README
+++ b/extras/data_generation/structure_db/README
@@ -28,3 +28,13 @@ BUT BE AWARE, THE ACCORDING FREQUENCIES IN THE DATABASE WILL BE SET TO 0.0!
initial database generated in step 2:
use assign_structure_profiles.py to perform this task
+
+To qualitatively reproduce the default StructuralDB in ProMod3, you first
+perform step 1 and 2 with a non redundant set of protein structures as
+defined by PISCES with around 25000 chains (e.g. seq id threshold: 90,
+resolution threshold: 2.2).
+Repeat step 1 and 2 with a smaller PISCES list (5000-6000 entries,
+e.g. seq id threshold: 25 , resolution threshold: 1.8).
+The first database serves as default StructureDB and the second db as
+the source db for the structural profiles generated in steps 3-5.
+
--
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