[phenixbb] DEN refinement is crashing

[Jeff Headd]

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" <mariosan at gmail.com> wrote:

> 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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>
>
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