Commit 7bd92d97 authored by cmaffeo2's avatar cmaffeo2
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Improved cadnano segment protocol; using 1.03 instead of 1 for max beads,...

Improved cadnano segment protocol; using 1.03 instead of 1 for max beads, resulting in more 1-bp beads
parent ed819c4b
......@@ -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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