[phenixbb] DEN refinement is crashing

Mario Sanches mariosan at gmail.com
Mon Apr 2 08:21:33 PDT 2012


An update on the DEN job I was running last Friday:

It went to completion. However, the Rwork/Rfree where higher than what I
had before (original R + 20%). Since it is stil under development I will
not read to much into it and wait for a newer version :-)

I will be happy to provide the inputs if the developers want to use it on a
test.

Thank you again for your help,

Mario Sanches

On Fri, Mar 30, 2012 at 11:13 AM, Mario Sanches <mariosan at gmail.com> wrote:

> 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
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>
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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
>



-- 
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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