[phenixbb] DEN refinement is crashing
Mario Sanches
mariosan at gmail.com
Fri Mar 30 05:40:43 PDT 2012
I am running phenix.refine using the graphical interface. Under "global
refinement paramerters..." I am selecting "DEN". The problem is that
Python crashes all the time, always at the same point (see portion of the
log output below). Is it a known bug? Is DEN incompatible with some of the
options in refinement? My resolution is 2.9A by the way.
Thank you for your inputs.
Mario Sanches
___________________________
Log output final portion:
tardy dynamics:
number of bodies: 3678
number of degrees of freedom: 3713
number of atoms * 3: 38220
ratio: 0.097 = 1/10.29
temperature degrees of freedom: cartesian (38220)
kinetic energy sensitivity to generalized velocities:
n: 3713
min: 3.61771e-06
max: 0.0300001
mean: 0.00410663
time step: 0.00100 pico seconds
velocity scaling: True
suppressing allowed origin shifts: False
new target temperature: 2500.00 K
step= 1 temperature= 2500.0 rmsd=0.0446 r_work=0.3010 r_free=0.3214
--
Mario Sanches
Postdoctoral Researcher
Samuel Lunenfeld Research Institute
Mount Sinai Hospital
600 University Ave
Toronto - Ontario
Canada
M5G 1X5
http://ca.linkedin.com/in/mariosanches
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