From 7bd92d9734f13ac6aa60ab816fc205bb11fb87d6 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 13 Jul 2018 18:45:04 -0500
Subject: [PATCH] Improved cadnano segment protocol; using 1.03 instead of 1
for max beads, resulting in more 1-bp beads
---
cadnano_segments.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/cadnano_segments.py b/cadnano_segments.py
index e261920..585b368 100644
--- a/cadnano_segments.py
+++ b/cadnano_segments.py
@@ -625,7 +625,7 @@ def run_simulation_protocol( output_name, job_id, json_data,
simargs['timestep'] = 50e-6
model._update_segment_positions(coordinates)
model._clear_beads()
- model._generate_bead_model( 1, 1, local_twist=True, escapable_twist=True )
+ model._generate_bead_model( 1.03, 1.03, local_twist=True, escapable_twist=True )
model.simulate( outputPrefix = output_prefix, numSteps=fine_steps, **simargs )
coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.0.dcd' % full_output_prefix, rmsdThreshold=1)
--
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