[phenixbb] DEN refinement is crashing

[Mario Sanches]

Thank you Nat and Jeff for your responses.

I was using the latest stable PHENIX version but now downloaded the
latest nightly build. It seems to be running fine now, even thought he job
is still running. I will let you know of the output once it is finished.

Thank you again,

Mario Sanches

On Fri, Mar 30, 2012 at 10:20 AM, Jeff Headd <jjheadd at lbl.gov> wrote:

> 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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-- 
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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