[phenixbb] DEN refinement is crashing

Mon Apr 2 14:46:25 PDT 2012

I've been having the same problem. No matter what settings I use my final R factors are a lot higher than the starting ones. Using default settings they blow up from 31/32 to 50/60 :/ I've gotten them back down to 35 with cartesian annealing but they are still higher than the starting ones and the maps are not any better. With the torsion annealing I can lower them by lowering the starting temperature but even if I go down to 1000K they are still higher than what I start with. I usually optimize both gamma and weight automatically too... 

I tried running it with individual sites/individual adp with/and without NCS (trying both cartesian and torsion). I also tried using homologous reference models solved at higher resolution... 

If you come up with suggestions for what else to try I would love to hear them :)

cheers,
Melania

On Apr 2, 2012, at 8:45 AM, Mario Sanches wrote:

> 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
> 
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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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