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@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@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@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

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