[phenixbb] DEN refinement is crashing

[Mario Sanches]

Hi Jeff,

I ran it with XYZ and Individual B-factors refinement. I am sending you the
inputs right now so you can do a test.

Thanks again,

Mario Sanches


On Mon, Apr 2, 2012 at 11:39 AM, Jeff Headd <jjheadd at lbl.gov> wrote:

> 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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>


-- 
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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