[phenixbb] DEN refinement is crashing

Jeff Headd jjheadd at lbl.gov
Mon Apr 2 08:39:26 PDT 2012


Hi Mario,

Did you run your DEN refinement with optimization? If not, that could
explain the behavior. It could also be the default refinement settings.

I would be interested in your input files to see why your R values are
going up so much, but hopefully with better defaults this won't happen.

Jeff
On Apr 2, 2012 11:23 AM, "Mario Sanches" <mariosan at gmail.com> wrote:

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