[phenixbb] Is DEN refinement working?

Jeff Headd jjheadd at lbl.gov
Fri Jun 28 19:29:33 PDT 2013

Hi Jamie,

That sounds to me like your job has hung for some reason. It should say
that it is running simulated annealing, and should have lines in the log
such as "...trying gamma 0.500000, weight 30.000000" to indicate that
gamma/weight pair has been started. The coordinate minimization step is
usually quite fast, even for large structures.

What version of Phenix are you using? It would be worth trying to run:

libtbx.python /path_to_phenix/phenix_regression/den_restraints/tst.py to
see if DEN works correctly on your system. That should complete in under a


On Fri, Jun 28, 2013 at 4:46 PM, Wallen, Jamie <jwallen at biochem.wustl.edu>wrote:

>  Hello All,
>  I am trying to use DEN refinement to refine a low resolution (5A)
> structure. I was able to succesfully start the run without crashes, and the
> run is currently going on 30 processors (I am trying to optimize the gamma
> and weight). My question is that the log file stopped not far in to the run
> and has not updated in 24 hours. The log file list every residue in my
> structure, and the last line simply says :
>    ----------coordinate minimization before annealing----------
>  According to the computer cluster, the job is still running. I wanted to
> ask if this is OK or if it has stalled? Thanks.
>  Jamie
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20130628/c731afb0/attachment.htm>

More information about the phenixbb mailing list