[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
M5G 1X5
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