Hi Mario,
I've not encountered that bug before, but as Nat said I would suggest
trying a more recent installer if you have not.
If you still encounter crashes, could you send me your input files off-list
so I could try to replicate the problem here? Everything will be kept
confidential.
As an aside, DEN refinement will soon be separated out as its own program,
with GUI, to allow for more sensible default parameters and directed
control.
Thanks,
Jeff
On Mar 30, 2012 5:42 AM, "Mario Sanches"
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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