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

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)